HARRISBURG, Pa. — Former Penn State President Graham Spanier was arraigned and released on bail at a brief court appearance Wednesday on charges he lied about and concealed the child sex abuse allegations involving former assistant football coach Jerry Sandusky.

Spanier, accompanied by his wife, signed paperwork after his bail was set at $125,000 unsecured and left a Harrisburg district justice's office where two co-defendants were arraigned last week.

After the court appearance, Spanier's attorney, Elizabeth Ainslie, proclaimed Spanier's innocence and called prosecutors' claims he was part of a conspiracy of silence "ridiculous."

Spanier, 64, was charged last week with perjury, obstruction, endangering the welfare of children, failure to properly report suspected abuse and conspiracy for his actions in response to complaints about Jerry Sandusky showering with children. Spanier denies the allegations and has claimed he is being framed for political purposes.

Earlier: Penn St.'s ex-president charged in Sandusky scandal

He served as Penn State's president for 16 years but was forced out a year ago after Sandusky was charged along with two of Spanier's top underlings. Spanier is on paid leave as a member of the faculty.

Craig Houtz / Reuters file

Former Penn State University President Graham Spanier, left, and Second Mile founder and former Penn State assistant football coach Jerry Sandusky, attend the Second Mile Celebrity Golf Classic, in State College, Pennsylvania, in 1997.

Along with the charges against Spanier, prosecutors added counts against Tim Curley and Gary Schultz. They were arraigned Thursday. Curley, the athletic director on leave, and Schultz, the school's retired vice president, await trial in January on charges of failure to report suspected abuse and perjury.

The new charges came almost exactly a year after details of the case against Sandusky sent a maelstrom through State College, toppling longtime head coach Joe Paterno and eventually leading to severe NCAA sanctions against the football team.

Sandusky, 68, vigorously contested the charges but was convicted in June of 45 counts of abuse of boys, including violent sexual attacks inside campus facilities. He was sentenced last month to 30 to 60 years in prison.

A grand jury report alleged Spanier testified falsely that he did not know of a 1998 complaint against Sandusky, made by a mother and investigated by university police.

Full coverage of the Sandusky trial

"Spanier was obviously kept in the loop on this matter as Schultz copied him in on emails that discussed the status and conclusion of the investigation," the jury report said.

It also claimed Spanier lied about a 2001 instance of abuse witnessed by a graduate assistant, when he testified that Curley and Schultz described it only as horseplay. Email traffic among the men, jurors wrote, "make clear they are discussing an event that involves the abuse of a child."

Spanier's obstruction charges involve "numerous lies" and hiding "pertinent files and notes," alleged the grand jury report, known as a presentment.

Watch US News crime videos on NBCNews.com 

The report described how he addressed the growing scandal last year with the board of trustees, and how he put out statements supportive of Curley and Schultz after their arrest. The jury report said investigators were immediately able to get important records from the university after Spanier was replaced as president.

"It should be noted that Spanier continues to mislead with numerous public statements that contain demonstrably false statements," the jury claimed.

Spanier's lawyers put out a written statement law week that accused Gov. Tom Corbett, who was attorney general when the investigation began, of orchestrating the charges to divert attention from questions about why it took three years to bring charges against Sandusky. They said there was no factual basis for the Spanier charges.

"Spanier has committed no crime and looks forward to the opportunity to clear his good name and well-earned national reputation for integrity," his defense lawyers wrote. "This presentment is a politically motivated frame-up of an innocent man."

Attorney General Linda Kelly said last week the three administrators had engaged in a "conspiracy of silence" to hide the truth.

Stay informed with the latest headlines; sign up for our newsletter

More content from NBCNews.com:

• 6 splitting headaches waiting for Obama
• Nor'easter threatens up to foot of snow in Sandy's wake
• Cops: Co-worker kills 2, wounds 2 at chicken processing plant
• Michigan highway shootings suspect arrested
• Underwear needed for Staten Island victims of Sandy, official says
• Nun accused of stealing $128,000 to play casinos

Follow US news from NBCNews.com on Twitter and Facebook

Updated at 2:20 p.m. ET: Pennsylvania state prosecutors, citing what they called "a conspiracy of silence," on Thursday charged Graham Spanier, the former president of Penn State University, with perjury, obstruction of justice and endangering the welfare of children abused by the school's former defensive coordinator, convicted child molester Jerry Sandusky. 

The prosecutors also brought new felony charges against two former top Penn State officials -- Tim Curley, the ex-athletic director, and Gary Schultz, an ex-Penn State vice president who oversaw the campus police. Both men had been previously charged in the case and they, along with Spanier, have publicly insisted on their innocence.

"This case is about three powerful men who held high positions -- three men who used their positions to conceal and cover up for years the activities of a known child predator," state Attorney General Linda Kelly said at a news conference in Harrisburg. "This was not a mistake, an oversight or a misjudgment.

"This was a conspiracy of silence by top officials at Penn State, working to actively conceal the truth, with total disregard to the suffering of children,"  Kelly said.

“Graham Spanier has commited no crime and looks forward to the opportunity to clear his good name and well earned national reputation for integrity,” Spanier’s lawyers said in a statement. “This presentment is a politically motivated frame-up of an innocent man. And if these charges ever come to trial, we will prove it.”

“To be clear, Tim Curley is innocent of all charges.
We are carefully reviewing the presentment and will reserve a more comprehensive comment for a later time,” Curley’s lawyer said in a statement.

They also blamed the charges against their client on Pennsylvania’s Republican Gov. Tom Corbett, saying that Kelly – whom he appointed – had brought the case against Spanier to divert attention from the fact that when Corbett was attorney general, he had failed to bring criminal charges against Sandusky in 2009  – an issue that Democrats have criticized him for. Kelly on Thursday adamantly denied that politics played any role in the case.

The new charges come nearly one year after Sandusky was arrested and charged with repeatedly abusing young boys dating back to 1998, setting off one of the biggest scandals in the history of college sports. Sandusky, the longtime deputy to the school's late legendary football coach, Joe Paterno, was convicted on 45 counts of child sex abuse last June and was sentenced last month to 30 to 60 years in state prison.

Full coverage of the Sandusky trial

Spanier, 64, a professional sociologist and family therapist, served for 16 years as president of Penn State, one of the largest public universities in the country, where he was a popular figure on campus and an active booster of the school's football program. He was fired last year, after Sandusky’s arrest, and is now facing eight criminal charges, including five felonies, each of which carry a potential prison term of seven years.

The charges laid out in a new 39-page grand jury presentment are based in part on evidence uncovered in a report last summer by former FBI director Louis Freeh. But the grand jury report also provide new details-- in part culled from previously undisclosed grand jury testimony and documents -- of how Spanier, Schultz and Curley allegedly deceived investigators and hid key information from other university officials, including the chief of the campus police and, in Spanier's case, from the Penn State Board of Trustees.

The grand jury report also provides new details about the trail of an incriminating "Sandusky file" that was kept in a file drawer in Schultz's office -- documenting a 1998 police investigation of Sandusky "with very detailed information" about Sandusky's contact with a young boy in the Penn State shower and a later 2001 allegation about Sandusky abusing another young boy in the Penn State shower.

This and other material was not turned over to prosecutors despite  grand jury subpoenas for all documents relating to the defensive coordinator between 2010 and April 2012. In all, 22 boxes of Sandusky documents, photographs and other materials were not initially turned over in response to the subpoeanas and, as a result, the investigation into Sandusky was "signficantly thwarted and frustrated," the grand jury report states.

According to the new grand jury report, the Sandusky file was removed from Schultz's office by his administrative assistant last year and delivered to his home on Nov. 5, 2011, the same day the then-Penn State vice president was first charged in the case. A previous assistant testified she was given an "unusual request" by Schultz to never "look in" the Sandusky file and that the request was delivered in a "tone of voice" she had never heard him use before.

The new grand jury report states that the emails and other documents show that Spanier, Curley and Schultz at first agreed to report to child welfare authorities a 2001 allegation by former graduate assistant Mike McQueary that he saw Sandusky sexually abusing a young boy in the Penn State shower. One indication of how serious they took it was found in documents showing that Schultz sought legal advice from Penn State's outside lawyer, Wendell Courtney, who billed the school for a "Conference with G Schultz re reporting of suspected child abuse."

But Curley later changed his mind "after talking it over with Joe" -- a reference to the late coach Joe Paterno. (At the news conference, Kelly declined to speculate on whether Paterno would have been charged in the case had he been alive.) They then developed a new plan to encourage Sandusky to seek professional help. "This approach is acceptable to me," Spanier wrote in a Feb. 27, 2001, email to Curley and Schultz.

Spanier added: "The only downside for us if the message isn't 'heard' and acted upon, and we then become vulnerable for not having reported it. But that can be assessed down the road. The approach you outline and a reasonable way to proceed."

According to the new grand jury report, Spanier initially told investigators in March 2011 that he knew nothing about the 1998 police probe of Sandusky (despite emails showing he was briefed on the investigation) and was given only sketchy information about the 2001 allegation, believing that involved only a contention of Sandusky "horse playing around" with a child. And he later made similar comments before a grand jury, including testifying  that there was "no discussion" about reporting the 2001 incident to child welfare or police -- part of the basis for the perjury charge against him.

The report says that Spanier never told the Penn State trustees about either the 1998 or 2001 allegations. When he did brief the board in May 2011 -- after a newspaper story first disclosed the investigation into Sandusky -- Spanier directed the university's chief lawyer, Cynthia Baldwin, to leave the room and then "specifically informed the Board that the investigation had nothing to do with Penn State and that the investigation was regarding a child in Clinton County [Pennsylvania] without affiliation with Penn State," the grand jury report states. 

More content from NBCNews.com:

• NBC/WSJ/Marist polls: Obama leads in Iowa, running neck and neck in NH, Wis.
• 'Pure mayhem' as New York City tires to get back to work
• Campaign ad spending closes in on $1 billion
• Cops: At least 3 shot during Hollywood Halloween celebrations
• Diesel spill pollutes waters between Staten Island, NJ
• 2 children stabbed to death in Ill. home; victim's mom in custody

Follow US news from NBCNews.com on Twitter and Facebook

Reuters file

Penn State University President Graham Spanier, left, and Jerry Sandusky attend the Second Mile Celebrity Golf Classic, in State College, Penn. in 1997.

Of four former top Penn State employees accused by an independent investigation of concealing sexual abuse by Jerry Sandusky, one is dead and two are facing charges of perjury and not reporting abuse.

The fourth, former university president Graham Spanier, remains on the Penn State staff and hasn't been charged.

But a report published Thursday on what went wrong at Penn State outlines Spanier's actions and could increase the likelihood that prosecutors will pursue criminal charges against him as well, a legal expert said.

Follow @msnbc_us

Follow Kari Huus on Twitter and Facebook.

"Do I think he will face further ramifications?" said Drexel University law professor Dan Filler. "He’s definitely at risk."

The 276-page report on the findings from of a special investigation led by Louis Freeh emphasizes the roles of "the four most powerful people" at Penn State "who failed to protect against a child sexual predator harming children for over a decade."

That lumps Spanier with former Penn State vice president Gary Schultz and former university athletic director Timothy Curley, and former head football coach Joe Paterno, who died in January. Schultz and Curley are accused of failing to report the allegations of sexual abuse by Sandusky, and of committing perjury when questioned by a grand jury.

Penn State report: What it says about Sandusky’s associates

These men "concealed Sandusky’s activities from the Board of Trustees, the University community and authorities," concluded Freeh, who was hired by Penn State to conduct the investigation.

Spanier rejected that accusation.

"Unfortunately, Judge Freeh's conclusion …  that Dr. Spanier was engaged in a course of 'active concealment' is simply not supported by the facts or by the report itself," said a statement Spanier issued Thursday through his attorneys, Peter Vaira and Elizabeth Ainslieon Thursday.

Sandusky, 68, was arrested in November 2011 and found guilty of 45 counts of child sexual abuse. He is in jail awaiting sentencing.

The Freeh report looked into the role of individuals and the institution of Penn state in failing to stop Sandusky. It says Sandusky assaulted boys on university property and focused on two incidents — a 1998 sexual abuse complaint that was investigated by police and a 2001 eyewitness report of Sandusky apparently involved in sexual activity with a 10- to 12-year-old boy in a shower.

The statement from Spanier’s lawyers repeated his claim that he was never contacted by law enforcement or other officials about criminal conduct on the part of Sandusky.

"As he told Judge Freeh himself last Friday and has steadfastly maintained, at no time in his 16 years as President of Penn State was Dr. Spanier told of any incident involving Jerry Sandusky that described child abuse, sexual misconduct, or criminality of any nature."

Email conversations documented by the report seem to suggest that Spanier was informed by Shultz about the 1998 investigation of Sandusky, which arose after a mother alleged that the coach sexually assaulted her 11-year-old son in a shower.

The notes reveal little about Spanier’s reaction to the investigation and no record to suggest that he or the others addressed Sandusky about the allegations.

The report documents how, after witnessing Sandusky in sexual activity with a child in the locker room showers on campus in 2001, graduate assistant Mike McQueary reported it to coach Joe Paterno, who passed that information on to Curley and Shultz, who brought it to Spanier.

There is no record of Spanier speaking directly to McQueary.

"(Spanier's) biggest defense is he didn’t hear it from McQueary," said Filler. "He heard it from Curley and Schultz."

The report did not make clear how McQueary's story was spelled out to Spanier, but it says that records show that Curley, Schultz and Spanier devised a plan to tell Sandusky they thought he had a problem, offer him professional help and advise him not to bring children into campus facilities.

In email cited by the report, Spanier agrees with this approach, which he calls "humane and reasonable."

"The only downside for us is if the message isn’t 'heard' and acted on, and we become vulnerable for not having reported it. But that can be assessed down the road," he said in the email.

No one reported the alleged rape of the boy to the police and there is no record suggesting that they attempted to identify the boy or find out if he had been harmed, the report said.

Spanier also did not report the incident to the Board of Trustees at the time, only doing so under pressure after he was called to testify before the grand jury in the Sandusky case, along with Curley and Schultz, the report said.

The report does not accuse Spanier of lying but it does provide fodder for a prosecutor to probe inconsistencies in Spanier’s statements, raising the risks of charges for the former university president, said Filler.

"If prosecutors decide he lied under oath and they can prove it, that's where his risk is," he said. "As with other cases -- like the Clinton case — it’s often not the bad conduct. It’s the lying under oath."

Another possible risk to Spanier, said Filler, is the possibility that Shultz and Curley strike a plea deal in exchange for damning testimony against Spanier.

The report says Spanier resisted independent investigation of Sandusky, "discouraged discussion and dissent" and had "a striking lack of empathy for child abuse victims."

"Spanier just does not go to the board with anything," said Filler. "That may not be criminal, but boy that is ugly for lots of reasons. He has a duty to bring risks to the university to the board, and he doesn’t."

Moreover, Filler said, the comprehensiveness and caliber of the Freeh report — led by former U.S. attorney, FBI director and federal judge — provides investigative legwork for any potential prosecutor.

"The report isn’t evidence," said Filler. "But it makes it easy for a prosecutor to see what there is. And it does change the politics of the decision to prosecute. And (prosecutors) are elected officials, they are sensitive to this."

More content from msnbc.com and NBC News:

• Horrific N.J. car accident becomes red-light stop campaign
• Man becomes cop to honor murdered brother
• Poll: Confidence in organized religion at all-time low
• Survivalist made chilling video before killing wife, daughter
• Caught on camera: Shark steals fish off pole

Follow US News on msnbc.com on Twitter and Facebook

Follow Kari Huus on Facebook

Gary Cameron / Reuters file

Former FBI Director Louis Freeh was hired in November to determine whether Penn State University officials knew about child sex abuse allegations against former assistant football coach Jerry Sandusky.

The results of an internal investigation of Pennsylvania State University’s response to child sexual abuse allegations against former assistant football coach Jerry Sandusky will be made public on Thursday.

An announcement Tuesday indicated a report on the investigation led by former FBI chief Louis Freeh would be posted online Thursday at 9 a.m. ET. It said Freeh would hold a news conference an hour later to discuss its findings and recommendations.

“We look forward to seeing the report on Thursday and reviewing Judge Freeh's recommendations,” said Penn State spokesman David La Torre. “The university will provide a response in Scranton on Thursday at a time and location to be announced.”

Sandusky, 68, was found guilty of 45 counts of child sexual abuse last month and is currently in prison awaiting sentencing. He faces a maximum sentence of more than 400 years in prison.

Freeh was hired by the university in November to review of the university's dealings with Sandusky and its response to a 2001 report that he sexually abused of a boy in a Penn State shower room, an incident witnessed by football assistant Michael McQueary.

Former Penn State President Graham Spanier has come under particular scrutiny in recent weeks amid news reports suggesting that he was made aware of suspicious activity involving Sandusky in 2001 and that no report of the incident was made to authorities.

Citing emails obtained by Freeh’s investigators, CNN reported last week that Spanier and two other university officials — Gary Schultz, the former senior vice president of finance and business, and Tim Curley, the athletic director on administrative leave — agreed to take a "humane" approach in dealing with  Sandusky following his alleged sexual encounter with a boy.

Instead of reporting the incident to police, according to the report, administrators instead planned to ask Sandusky to seek counseling and said they would tell officials at the Second Mile, the charity he founded and where he met many of the children he would later abuse, about their concerns.

Related stories

Matt Sandusky: From staunch defender to father's most damning accuser

Ghosts of Sandusky's dreams haunt empty house where his charity was born

Attorneys for Spanier fired back earlier Tuesday, saying their client was never informed about the shower room incident involving Sandusky.

"At no time in the more than 16 years of his presidency at Penn State was Dr. Spanier told of an incident involving Jerry Sandusky that described child abuse, sexual misconduct or criminality of any kind, and he reiterated that during his interview with Louis Freeh and his colleagues,'' Spanier's attorneys, Peter Vaira and Elizabeth Ainslie, said in a written statement.

In addition, Freeh’s report is expected to include information about the actions of former head football coach Joe Paterno in the wake of McQueary’s allegations. Paterno, a legend in college football, died of lung cancer in January at 85.

In a statement Tuesday, Paterno's family also pushed back against the leak of emails to CNN, including one in which Curley stated, "After giving it more thought, and talking it over with Joe yesterday - I am uncomfortable with what we agreed were the next steps."

"The media spin that this is proof of some sort of cover up is completely false," the statment said. "When the facts come out, it will be clear that Joe Paterno never gave Tim Curley any instructions to protect Sandusky or limit any investigation of his actions.

"Joe Paterno did not cover up for Jerry Sandusky.  Joe Paterno did not know that Jerry Sandusky was a pedophile.  Joe Paterno did not act in any way to prevent a proper investigation of Jerry Sandusky.  To claim otherwise is a distortion of the truth.

The Sandusky scandal led to the ouster of Spanier and Paterno and charges against Curley, who is on leave from the university, and Schultz, who has since retired.  The latter two are accused of perjury for their grand jury testimony and failing to properly report suspected child abuse.

Spanier hasn't been charged.

Chip Bell, Tom Winter and Julmary Zambrano of NBC News and the Associated Press contributed to this report.

More content from msnbc.com and NBC News:

• Farmer says Arkansas drought turns cattle ranch into 'desert'
• Deadly black lung surges in coal country
• Barbecue brush bristle in man's intestine
• Video: Alligator bites of Florida teen's arm
• Hiker awaiting help for broken leg ends up rescuing his rescuer

Follow US News on msnbc.com on Twitter and Facebook