Max Rossi / Reuters

Pope Francis, shown Sunday, reaffirmed the church's official criticism of the group representing most U.S. nuns as having 'radical feminist' doctrine.

VATICAN CITY -- Pope Francis has reaffirmed the Vatican's criticism of a body that represents U.S. nuns that the Church said was tainted by "radical" feminism, dashing hopes that he might take a softer stand with the sisters.

Francis's predecessor, Benedict, decreed that the Leadership Conference of Women Religious (LCWR), a group that represents more than 80 percent of the 57,000 Catholic nuns in the United States, must change its ways, a ruling that the Vatican said on Monday still applied.

Last year, a Vatican report said the LCWR had "serious doctrinal problems" and promoted "radical feminist themes incompatible with the Catholic faith," criticizing it for taking a soft line on issues such as birth control and homosexuality.

The nuns received wide support among American Catholics, particularly on the liberal wing of the church, as LCWR leaders travelled around the United States in a bus to defend themselves against the accusations.

On Monday the group's leaders met Archbishop Gerhard Ludwig Mueller, the new head of the Vatican's doctrinal department, and Archbishop Peter Sartain of Seattle, who has been assigned by the Vatican to correct the group's perceived failings.

"Archbishop Mueller informed the (LCWR) presidency that he had recently discussed the doctrinal assessment with Pope Francis, who reaffirmed the findings of the assessment and the program of reform, " the Vatican's statement said.

The Vatican reminded the group that it would "remain under the direction of the Holy See," the statement said.

It was the nuns' first meeting with Mueller, who succeeded American Cardinal William Levada as head of the Congregation for the Doctrine of the Faith. Levada, who retired last year, oversaw the Vatican's investigation of the U.S. nuns.

A statement from the LCWR said the "conversation was open and frank" and added: "We pray that these conversations may bear fruit for the good of the Church."

In April 2012, the doctrinal department criticized the LCWR for challenging bishops and for being "silent on the right to life," saying it had failed to make the "Biblical view of family life and human sexuality" a central plank of its agenda.

The nuns supported President Barack Obama's health-care reform, part of which makes insurance coverage of birth control mandatory, while U.S. bishops opposed it.

Many nuns said the Vatican's report misunderstood their intentions and undervalued their work for social justice.

Supporters of the nuns said the women had helped the image of the church in the United States at a time when it was engulfed in scandal over sexual abuse of minors by priests. They were praised by many fellow Catholics and the media for their work with the poor and sick.

Monday's Vatican statement expressed gratitude for the "great contribution" American Catholic nuns had made in teaching and caring for the sick and poor.

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John Makely / NBC News

Danny Peterson is a seminarian attending the Immaculate Conception Seminary located on the Seton Hall University campus in South Orange, N.J.

Half a world away from where Catholic cardinals gathered this week to elect Pope Francis, men who hope to do the daily work of the faith woke up at the Immaculate Conception Seminary in South Orange, N.J., and met for pre-sunrise prayers.

Fifty-seven aspiring priests from around the world live in the seminary on the campus of Seton Hall University. They will spend from six to eight years undergoing the process of formation before becoming full priests in the archdiocese of Newark, which has 238 parishes over four counties.

Afflicted by scandal and battling decreased enthusiasm in the United States and Europe, the church will rely on men such as these in coming decades to maintain the faith. The pope himself alluded the challenges on Friday, urging cardinals to never "give in to the pessimism, to that bitterness, that the devil places before us every day."

Danny Peterson, of Richmond, Va., knows most of his peers do not want to become men of the cloth. A surfer who studied international affairs, the 28-year-old used to pack an ice chest of beers for football games and concerts. No longer.

“I’m not going to see Pearl Jam anymore,” Peterson says. “Those days are over.” Peterson sees himself in what he calls the “John Paul II generation” – a cohort of younger Catholics inspired by the charismatic deceased pontiff. At 14, he saw John Paul II at a World Youth Day celebration in Rome. He’s traveled all over the world, from Haiti to Ecuador to the Czech Republic. This winter, he sold his old surfboard for $400 to fund a ski trip – a hefty sum considering he stretches out two stipends of $500 each year.

Becoming a priest was always on the table in his large Catholic family which includes five older brothers and sisters, Peterson said. His father briefly spent time in the seminary before meeting Peterson’s mother. His family has supported his choice, he said. He’s heard other reactions from friends, including: “You’re an effing idiot.”

“It’s hard here,” Peterson said of the seminary life. “We don’t have a lot of money. The room is the size of a closet. If I didn’t think I was called to do it I would have left already.”

John Makely / NBC News

Nelson Oyola, a seminarian attending the Immaculate Conception Seminary, sets the chapel up for an afternoon mass.

The average age for new priests in 2012 was nearly 35, according to a review conducted by the Center for Applied Research in the Apostolate at Georgetown University. Thirty percent of new priests were born outside the United States. More than half had more than two siblings.

American-born and opinionated, Peterson is one model for what the next wave of American priests may look like. Nelson Oyola, 31, is another.

Oyola’s day begins with a class quiz on the laws of the church. There are heads with more than a few gray hairs in his classes, and several Spanish speakers.

Oyola knew little English when he left his village outside Bogota, Colombia, nine years ago to pursue his dream of becoming a priest. Now, dressed all in black with a white roman collar that seminarians are allowed to wear only on campus, the soft-spoken student searches carefully for the right word.

“God was calling me to serve here,” Oyola says. “It was something in me. I always saw myself celebrating Mass.” As with many priests, the voices of loved ones also helped when choosing a life that includes celibacy, little money, and late-night visits to hospital beds.

John Makely / NBC News

Peterson prepares for class.

Encouraged by his grandmother and a young local priest named Father Julian, Oyola never felt that aspiring to become a priest was a strange ambition for a young man.

Oyola had five girlfriends in high school. It’s good for a priest to know what it’s like to be a in a relationship, he said. The last girlfriend broke up with him as they approached the age young people often marry in Colombia. She knew his heart was set on the priesthood.

The Spanish-speaking congregations he has met at churches like St. Francis de Sales in Lodi and Our Lady of Mt. Carmel in Jersey City remind Oyola of home. At one point recently, there were 15 Colombians among the seminarians in South Orange. Every time a new Colombian arrives, he is brought by the group to the Statue of Liberty, Oyola said.

That God has called him to serve so far away from home does not make leaving his parents and two older brothers in Colombia any easier: “Every time the plane leaves, it feels like your heart stays on the ground.”

“That’s something that’s always on my mind,” Oyola said. “What if I don’t get to spend any time with them any more?” When he saw his cousin’s newborn, he wondered what a baby of his own would look like. “But I live with joy and no regrets,” Oyola said.

As the seminarians lined up to engage in a special vigil they held for as long as the conclave continued, they were aware that the church’s problems – ongoing revelations of sex abuse, a top-secret dossier on corruption in the church – would not go away with a new pope. The seminarians gathered around a big-screen TV to watch Pope Francis’ first appearance on Wednesday, Peterson said.

“We used to say that Latin America was the hope for the Catholic church,” Oyola said. “Now I realize that maybe we are not the hope anymore. We are the present.”

Slideshow: Electing a pope

Cardinals from around the world gather in the Vatican to elect the next leader of the Roman Catholic Church.

Launch slideshow

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AP

Cardinals attend a meeting, at the Vatican, Monday, March 4, 2013.

As Roman Catholic cardinals convene in Rome to elect a new pope, American Catholics say that the sex abuse scandal is the most important issue facing the church today, according to a new poll.

Thirty-four percent of Catholics in the United States chose sex abuse or pedophilia in a poll by the Pew Forum on Religion and Public Life that was released on Wednesday. The poll was conducted Feb. 28 through March 3. Benedict XVI, now pope emeritus, left the Vatican for the papal retreat of Castel Gandolfo last Thursday.

Nine percent of respondents said they thought the church suffered from low credibility, and seven percent said they felt the church was not modern enough, according to the Pew poll.

What wasn’t on the minds of Catholics? The abdication of the pontiff, a development unprecedented in modern times. Only one-in-twenty Catholics said they considered the lack of a pope among the most pressing issues facing the faith.

Asked what the Catholic Church’s most important contribution to society is, 27 percent of adherents said charitable works including service to the poor, sick, and needy, the Pew survey found. Eleven percent said that moral guidance is the church’s greatest contribution.

The specter of sex abuse has followed numerous cardinals to the Holy See. Cardinal Roger Mahony of Los Angeles will be among those electing the next pope, despite revelations of abuse under his watch. Recently revealed documents show that Mahony helped to conceal the activities of abuser priests, the Los Angeles Times reported.

Another cardinal, New York City Archbishop Timothy Dolan, was deposed shortly before leaving for the conclave in an ongoing case involving the archdiocese of Milwaukee, which Dolan used to head. Hundreds of people have claimed that they were molested by priests in the archdiocese.

A recent New York Times / CBS News poll also found that the sex abuse scandal was foremost in the mind of American Catholics, with seven out of 10 respondents saying that American Catholic church has done a poor job of handling the crisis. In that poll, a majority said that the way the church has dealt with the issue has caused them to question the Vatican’s authority, according to the New York Times.

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LOS ANGELES -- Los Angeles police are combing through some 12,000 pages of priest abuse records released last week by the city's Catholic archdiocese to determine whether to open any new criminal investigations, authorities said Tuesday.

Many of the cases detailed in the more 120 personnel files were already known to law enforcement, a Los Angeles Police Department spokesman said, and others could not be prosecuted because the statute of limitations had run out.

Don Bartletti / Pool via Reuters, file

Cardinal Roger Mahony, shown in 2010, was stripped of all public and administrative duties after being linked to efforts to conceal child sexual abuse by priests. Police are using 12,000 pages of documents released by the Archdiocese of Los Angeles to look for leads that could strengthen old cases or prompt new ones.

But detectives wanted to make sure no leads had been missed in documents made public by the archdiocese as part of a 2007 civil court settlement, officer Bruce Borihanh said.

"Now that the list is available we want to be proactive and look at that list," Borihanh said. He said that he was not aware of any specific case that investigators were focused on and that it was possible no new leads would be discovered.

The probe marks the latest development following Thursday's release of the files, which has already led Archbishop Jose Gomez to strip his predecessor, Cardinal Roger Mahony, of all public and administrative duties.

Mahoney's former top aide, Thomas Curry, also stepped down as bishop of Santa Barbara. Both men had been linked to efforts to conceal the abuse.

In further fallout, the Los Angeles Unified School District severed its ties on Monday with a priest who, the files show, was once accused of molesting a teenage girl.

Father Joseph Pina, 66, took a job working for the school district in 2002, several years after he resigned as a pastor and was placed on inactive leave by the church. An attorney for Pina has declined to comment to Reuters on the matter.

The Los Angeles archdiocese, which serves 4 million Catholics, reached a $660 million civil settlement in 2007 with more than 500 victims of child molestation in the biggest such agreement of its kind in the nation.

Mahony at the time called the abuse "a terrible sin and crime."

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Damian Dovarganes / AP

The entrance to the Cathedral of Our Lady of the Angels, headquarters for Roman Catholic Archdiocese of Los Angeles, is seen Jan. 21.

Retired Cardinal Roger Mahony and other top Roman Catholic Archdiocese of Los Angeles officials maneuvered behind the scenes to shield molester priests, provide damage control for the church and keep parishioners in the dark, according to church personnel files.

The confidential records filed in a lawsuit against the archdiocese disclose how the church handled abuse allegations for decades and also reveal dissent from a top Mahony aide who criticized his superiors for covering up allegations of abuse rather than protecting children.

Notes inked by Mahony demonstrate he was disturbed about abuse and sent problem priests for treatment, but there also were lengthy delays or oversights in some cases. Mahony received psychological reports on some priests that mentioned the possibility of many other victims, for example, but there is no indication that he or other church leaders investigated further.

"This is all intolerable and unacceptable to me," Mahony wrote in 1991 on a file of the Rev. Lynn Caffoe, a priest suspected of locking boys in his room, videotaping their crotches and running up a $100 phone sex bill while with a boy. Caffoe was sent for therapy and removed from ministry, but Mahony didn't move to defrock him until 2004, a decade after the archdiocese lost track of him.

"He is a fugitive from justice," Mahony wrote to the Vatican's Cardinal Joseph Ratzinger, who is now Pope Benedict XVI. "A check of the Social Security index discloses no report of his demise, so presumably he is alive somewhere."

Caffoe died in 2009, six years after a newspaper reporter found him working at a homeless mission two blocks from a Salinas elementary school.

Mahony was out of town but issued a statement Monday apologizing for his mistakes and saying he had been "naive" about the lasting impacts of abuse. He has since met with 90 abuse victims privately and keeps an index card with each victim's name in his private chapel, where he prays for them daily, he said. The card also includes the name of the molesting priest "lest I forget that real priests created this appalling harm."

"It remains my daily and fervent prayer that God's grace will flood the heart and soul of each victim, and that their life journey continues forward with ever greater healing," Mahony wrote. "I am sorry."

The apology stands in contrast to letters Mahony was writing to accused priests more than two decades ago.

In 1987, he wrote to the Rev. Michael Wempe — who would ultimately admit to abusing 13 boys — while the priest was undergoing in-patient therapy at a New Mexico treatment center.

"Each of you there at Jemez Springs is very much in my prayers and I call you to mind each day during my celebration of the Eucharist," Mahony wrote to the priest, adding that he supported him in the experience.

The church's sex abuse policy was evolving and Mahony inherited some of the worst cases from his predecessor when he took over in 1985, J. Michael Hennigan, an archdiocese attorney, said in a separate series of emails. Priests were sent out of state for psychological treatment because they revealed more when their therapists were not required to report child abuse to law enforcement, as they were in California, he said.

At the time, clergy were not mandated sex abuse reporters and the church let the victims' families decide whether to contact police, he added.

In at least one case, a priest victimized the children of illegal immigrants and threatened to have them deported if they told, the files show.

The files are attached to a motion seeking punitive damages in a case involving a Mexican priest sent to Los Angeles in 1987 after he was brutally beaten in his parish south of Mexico City.

When parents complained the Rev. Nicholas Aguilar Rivera molested in LA, church officials told the priest but waited two days to call police — allowing him to flee to Mexico, court papers allege. At least 26 children told police they were abused during his 10 months in Los Angeles. The now-defrocked priest is believed to be in Mexico and remains a fugitive.

The personnel files of 13 other clerics were attached to the motion to show a cover-up pattern, said attorney Anthony De Marco, who represents the 35-year-old plaintiff. In one instance, a memo to Mahony discusses sending a cleric to a therapist who also is an attorney so any incriminating evidence is protected from authorities by lawyer-client privilege. In another instance, archdiocese officials paid a secret salary to a priest exiled to the Philippines after he and six other clerics were accused of having sex with a teen and impregnating her.

The exhibits offer a glimpse at some 30,000 pages to be made public as part of a record-setting $660 million settlement. The archdiocese agreed to give the files to more than 500 victims of priest abuse in 2007, but a lawyer for about 30 of the priests fought to keep records sealed. A judge recently ordered the church to release them without blacking out the names of church higher-ups after The Associated Press and the Los Angeles Times intervened.

They echo similar releases from other dioceses nationwide that have shown how church leaders for decades shuffled problem priests from parish to parish, covered up reports of abuse and didn't contact law enforcement. Top church officials in Missouri and Pennsylvania were criminally convicted last year for their roles in covering up abuse, more than a decade after the clergy sex abuse scandal began to unfold in Boston.

Mahony, who retired in 2011 after 26 years at the helm of the 4.3-million person archdiocese, has been particularly hounded by the case of the Rev. Michael Baker, who was sentenced to prison in 2007 for molestation — two decades after the priest confessed his abuse to Mahony.

Mahony noted the "extremely grave and serious situation" when he sent Baker for psychological treatment after the priest told him in 1986 that he had molested two brothers over seven years.

Baker returned to ministry the next year with a doctor's recommendation that he be defrocked immediately if he spent any time with minors. Despite several documented instances of being alone with boys, the priest wasn't removed from ministry until 2000. Around the same time, the church learned he was conducting baptisms without permission.

Church officials discussed announcing Baker's abuse in churches where he had worked, but Mahony rejected the idea.

"We could open up another firestorm — and it takes us years to recover from those," Mahony wrote in an Oct. 6, 2000, memo. "Is there no alternative to public announcements at all the Masses in 15 parishes??? Wow — that really scares the daylights out of me!!"

The aide, Msgr. Richard Loomis, noted his dismay over the matter when he retired in 2001 as vicar for clergy, the top church official who handled priestly discipline. In a memo to his successor, Loomis said Baker's attorney disclosed the priest had at least 10 other victims.

"We've stepped back 20 years and are being driven by the need to cover-up and to keep the presbyteriate & public happily ignorant rather than the need to protect children," Loomis wrote.

"The only other option is to sit and wait until another victim comes forward. Then someone else will end up owning the archdiocese of Los Angeles. The liability issues involved aside, I think that course of complete (in)action would be immoral and unethical."

Mahony preferred targeted warnings at schools and youth groups rather than a warning read at Masses, Hennigan said. Parish announcements were made two years later.

Baker, who was paroled in 2011, is alleged to have molested 20 children in his 26-year career. He could not be reached for comment.

The files also show Mahony corresponded with abusive priests while they underwent treatment out of state and worked to keep them out of California to avoid criminal and civil trouble.

One case involved the Msgr. Peter Garcia, a molester whom Mahony's predecessor sent for treatment in New Mexico. Mahony kept Garcia there after a lawyer warned in 1986 that the archdiocese could face "severe civil liability" if he returned and reoffended. Garcia had admitted raping an 11-year-old boy and later told a psychologist he molested 15 to 17 young boys.

"If Monsignor Garcia were to reappear here within the archdiocese, we might very well have some type of legal action filed in both the criminal and civil sectors," Mahony wrote to the director of Garcia's New Mexico treatment program.

Mahony then sent Garcia to another treatment center, but Garcia returned to LA in 1988 after being removed from ministry. He then contacted a victim's mother and asked to spend time with her younger son, according to a letter in the file.

Mahony moved to defrock him in 1989, and Garcia died a decade later.

Two major Catholic institutions filed lawsuits on Monday challenging the Obama administration's mandate that religiously affiliated employers offer health insurance for their workers that includes coverage for contraception.

Jonathan Daniel / Getty Images

The University of Notre Dame filed a lawsuit in federal court challenging a Health and Human Services rule on contraceptives.

The Archdiocese of Washington, D.C., and the University of Notre Dame separately filed lawsuits in federal court challenging a Health and Human Services rule that would require them to offer coverage for contraception, the use of which runs contrary to Catholic teaching.

"For the first time in this country’s history, the government’s new definition of religious institutions suggests that some of the very institutions that put our faith into practice — schools, hospitals and social service organizations — are not ‘religious enough,'" said Cardinal Donald Wuerl, the archbishop of Washington, in a statement.

Father John Jenkins, the president of Notre Dame, said: "This filing is about the freedom of a religious organization to live its mission, and its significance goes well beyond any debate about contraceptives."

(Jenkins emphasized that the university's suit was not intended to prevent access to contraception or to prevent the government from providing services.)

The contraceptive regulation erupted into a political firestorm in February, when Republicans seized on the proposed regulation as an example of a government "assault" on religious liberty.

In the face of public pressure, President Barack Obama announced a compromise in which employers could opt against including coverage for contraception, but insurers would be required to provide the option of coverage of those services to employees who wanted it.

The proposal became a hot-button political issue in much of February, especially as Republicans in Congress and on the campaign trail sought to strengthen exemptions for religiously affiliated employers from regulations that conflict with their faith's official teaching.

Alberto Pizzoli / AFP - Getty Images file

Cardinal Bernard Francis Law prays during the Eucharistic celebration with the new cardinals on November 21, 2010 at St. Peter's basilica at The Vatican.

A Vatican crackdown launched last month on the largest leadership organization for U.S. nuns reportedly was spurred on by American Catholic officials worried the nuns aren't vocal enough on conservative social issues.

On April 18, after a three-year investigation, the Vatican’s doctrine watchdog appointed Archbishop J. Peter Sartain of Seattle to oversee the nuns' organization and reform its programs to adhere more closely to "the teachings and discipline of the Church." 

The issues raised by the Vatican include the nuns' lack of outspokenness on issues such as gay marriage, abortion and contraception. Another concern is related to the conferences organized by the group featuring "a prevalence of certain radical feminist themes incompatible with the Catholic faith."

In a statement, the Leadership Conference of Women Religious, an umbrella organization representing 80 percent of the 57,000 nuns in the U.S., said it had been "taken by surprise by the gravity of the mandate."

The Vatican’s initiative was triggered by U.S. Archbishop William E. Lori's petition to investigate the nuns, according to the National Catholic Reporter and the British Catholic weekly The Tablet. Lori was recently appointed by the pope to lead the Archdiocese of Baltimore.

According to those same reports, Cardinal Bernard F. Law -- disgraced former archbishop of Boston -- was "the person in Rome most forcefully supporting Bishop Lori’s proposal." After media reports revealed he had permitted priests accused of sexually molesting children to continue serving, Law resigned in 2002. Pope John Paul II appointed Law as archpriest of the Papal Basilica of St. Mary Major in Rome in 2004, but he resigned from this position in November 2011 when he turned 80, the age most cardinals retire. 

Stephen J. Boitano / NBC via Getty Images file

Archbishop William Lori

Other American churchmen in Rome, including Cardinal Raymond Burke and Cardinal James Stafford, reportedly backed the investigation, according to the Religion News Service. The probe was led by former archbishop of San Francisco Cardinal William Levada, who has served on the Vatican's doctrine congregation since 2005.

The U.S. Conference of Catholic Bishops would not comment on the role of U.S. priests in the investigation into the nuns.

The Americans in Rome wouldn't have had the authority to start the investigation themselves, but they could lobby the Congregation for the Doctrine of the Faith -- the Vatican's doctrine watchdog -- for it, religion journalist and Vatican expert David Gibson told msnbc.com. Cardinal Joseph Ratzinger was the head of this congregation before he was elected pope in 2005.

Gibson, a Religion News Service correspondent, said the crackdown shows that concerns about poverty and economic inequality are taking a backseat in the church.

“There’s so much riding on the gay marriage battle, and on abortion rights, and on contraception that [bishops] want everybody in the church to be doubling down on those issues and not being distracted by social justice,” Gibson told msnbc.com.

Bishops have been playing defense for years in the wake of the church's sexual abuse crisis, and Gibson said they've been looking for issues on which they can reassert their moral authority.

“These issues are ones they think they can do that on, so they really want to show that... they’re calling the shots,” he added.

The statement issued by the Vatican read that "while there has been a great deal of work on the part of LCWR promoting issues of social justice in harmony with the church's social doctrine, it is silent on the right to life from conception to natural death."

While church leadership traditionally focuses on matters of doctrine, nuns have long been the public face of the church in the United States. They run the schools and hospitals and are concerned with performing the gospel rather than just preaching it from the pulpit, Gibson said.

American Catholics are showing their support for the nuns, organizing vigils all over the country to advocate for the end of the crackdown. The Nun Justice Project is one organization standing with the nuns against what they call "a prime example of how the hierarchy in the Roman Catholic Church misuses its power to diminish the voice of women."

An online petition started by Nun Justice had garnered more than 41,000 signatures at the time this story was written. Sister Annmarie Sanders, director of communications for the LCWR, told msnbc.com the organization finds the public support "heartening."

The LCWR will meet starting May 29 to begin its discussion of the Vatican's  doctrinal assessment and the implementation plan put forth by the Holy See. The Vatican has the power to remove the official recognition of the LCWR.

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