In the fall of 2011, a key Boston police counterterror intelligence unit -- funded with millions of dollars in U.S. homeland security grants -- was closely monitoring anti-Wall Street demonstrations, including tracking the Facebook pages and websites of the protesters and writing reports on the potential impact on "commercial and financial sector assets" in downtown areas, according to internal police documents.

The police monitoring of the activities of Occupy Boston -- an off-shoot of the Occupy Wall Street protests that swept the country in 2011 -- came during a period after the U.S. government received the second of two warnings from the Russian government about the radical Islamic ties of alleged Boston Marathon bomber Tamerlan Tsarnaev.

Boston Police Commissioner Ed Davis told a congressional panel Thursday that his department was never alerted by any federal agency to the information about Tsarnaev, but added that it was "hard to say" whether it would have made any difference in preventing the bombing. FBI  officials have insisted that the intelligence about Tsarnaev was vague and uncorroborated and that their own assessment at the time produced no "derogatory" information that justified opening a full-scale investigation.

But the internal Boston police documents, recently obtained by a civil liberties group, could raise fresh questions about the role of Homeland Security-funded "fusion centers" like the Boston Regional Intelligence Center, or BRIC, which conducted the monitoring. The Boston unit  is one of 72 such units set up to collect, analyze and share intelligence about potential terror threats. While  Homeland Security Secretary Janet Napolitano has called the units “one of the centerpieces” of the nation’s counterterrorism efforts, congressional critics have questioned their effectiveness and accused them in some cases of writing "useless" reports that infringed on civil liberties.

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“They  were monitoring completely lawful activities,” said Mara Verheyden-Hilliard, executive director of the Partnership for Civil Justice, a civil liberties group that recently obtained the documents on the BRIC’s monitoring of Occupy Boston under the Freedom of Information Act. She said the BRIC monitoring was an example of the “vast expenditure of government money” to collect intelligence on activities unrelated to terrorism, in violation of First Amendment rights.

A Boston police spokeswoman said the department has changed its reporting procedures since the monitoring of the protests and emphasized that the BRIC is “about a lot more than terrorism.”

A Homeland Security official declined comment, saying the BRIC, like other fusion centers, was “locally owned and operated.” But the official noted that, just five days before the marathon bombing, the BRIC did produce an assessment for the event that, while concluding there was “no specific” or “credible” threat information, advised that “officials should be aware of a range of potential terrorist threats, from scattered unsophisticated attacks to dispersal of chemical or biological agents.” The assessment also identified the marathon finish line — where the bombing took place — as well as Fenway Park as “an area of increased vulnerability.”

The internal police documents about the activities of the BRIC show that on Sept. 30, 2011 — just two days after the second Russian warning about Tsarnaev was sent to the CIA — the Boston police unit was focused on an upcoming “Take Back Boston Rally” planned for the city’s Dewey Square.

“Approximately 100 people are listed as attending the Take Back Boston Rally on the event’s Facebook page and Occupy Boston organziers are encouraging people to attend it as well,” reads one BRIC report written by a U.S. homeland security official on Sept. 30, 2011. “The BRIC has received information that approximately 700 people will participate in the Take Back Boston march, with approximately 100 people staying to camp out as part of Occupy Boston.”

A follow-up report, three days days later, tracked the number of protesters, noting that “the size of the camp in Dewey Square has steadily grown over the weekend” and that “according to the group’s website” the demonstrators were planning two marches, including one to a “local media station, very likely to be Fox News Boston on Beacon Hill.”

Verheyden-Hilliard, whose group obtained the documents, said it was not surprising that the BRIC would be reporting such information since later documents appear to show Homeland Security officials requesting such data. In one “Daily Intelligence Briefing,” dated Oct. 21, 2011, the “Threat Management Division” of Homeland Security’s Federal Protective Service outlines a “template for creating the daily intelligence brief for your region” and then cites a “list of events we want to request” that officials submit “for daily briefing information.” Among the categories, in addition to reporting on domestic terrorist acts and “significant criminal activity” is one called “Peaceful Activist Demonstrations.”

In his testimony Thursday, Commissioner Davis acknowledged to a House committee that his department, which runs the BRIC, was never provided any of the intelligence from the FBI and CIA that Tsarnaev, a resident of Cambridge, had been twice flagged by the Russians as an Islamic radical with ties to “underground” groups in that country.

“We were not aware of the two brothers,” Davis said in response to questioning by Rep. Mike McCaul of Texas, chairman of the House Homeland Security Committee. “We were not aware of Tamerlan’s activities.”

Davis acknowledged that police counterterrorism detectives were assigned to an FBI Joint Terrorism Task Force (JTTF) -- a separate unit from the Homeland Security fusion centers that serves as the government's primary investigative arm for probing terror threats. An FBI agent at the Boston JTTF conducted an “assessment” of Tsarnaev in 2011 after the first warning about his ties was sent by Russia’s FSB intelligence service. The assessment found no “derogatory” information about Tsarnaev that justified conducting a formal investigation. Later information about Tsarnaev included a second Russian warning to the CIA on Sept. 28, 2011.

But while Boston police had access to the JTTF’s classified database, Davis said that his own officers assigned to the task force were never  specifically alerted to any the information about Tsarnaev. “They tell me they received no word about that individual prior to the bombing.”

FBI spokesman Jason Pack said Thursday that state and local members of the JTTF are “responsible for maintaining awareness of possible threats” in their areas and could have performed “customized key word searches” of the FBI database that would have yielded the information about Tsarnaev.

NBC News researcher Taylor Sears contributed to this report.

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A federal judge on Friday struck down gag orders imposed on companies that receive national security letters — the supersecret mechanism by which the FBI can get your private information without a warrant in the name of counterterrorism.

In a ruling filed Friday afternoon in San Francisco, U.S. District Judge Susan Illston declared the letters — which prohibit recipients from even acknowledging they have received them, much less discuss their circumstances — an unconstitutional violation of the First Amendment.

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Illston ordered the FBI to stop issuing the letters, known as NSLs,  and to stop enforcing the gag orders. She stayed enforcement of her ruling for 90 days to give the government time to appeal.

The Justice Department said it was studying the decision and had no immediate comment.

Read the full ruling (.pdf)

The letters have been the focus of intense controversy, with government officials calling them vital to fighting terrorism and civil liberties advocates calling them a gross infringement of Americans' rights.

While the letters have been part of federal law since the 1980s, their use grew rapidly after they were endorsed in the USA Patriot Act following the terrorist attacks of Sept. 11, 2001. FBI reports filed to Congress show the agency issued 16,511 NSLs in 2011, the latest year for which full data are available.

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The letters are an administrative way under the Electronic Communications Privacy Act for the FBI to order companies that provide any sort of communications services — phone companies, Internet service providers, banks and the like — to hand over information about their customers without court approval. 

They come with an indefinite secrecy order, preventing the companies from ever letting their customers know their information has been surrendered.

"We are very pleased that the court recognized the fatal constitutional shortcomings of the NSL statute," said Matt Zimmerman, a senior staff attorney for the Electronic Frontier Foundation, the civil liberties group that filed the case on behalf of a telecommunications client it can't name under the law.

"The government's gags have truncated the public debate on these controversial surveillance tools," Zimmerman said. "Our client looks forward to the day when it can publicly discuss its experience."

Illston concluded that the secrecy provision couldn't be separated from the main body of the law because Congress meant for the letters to remain secret. She concluded that the entire section of that law governing the letters was unconstitutional.

"The government has a strong argument that allowing the government to prohibit recipients of NSL's from disclosing the specific information sought in NSL's to either the targets or the public is generally necessary to serve national security in ongoing investigations," Illston wrote. 

"However, the government has not shown that it is generally necessary to prohibit recipients from disclosing the mere fact of their receipt of NSLs."

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Zombies may have a tougher time taking over the world after a counterterrorism training program scheduled next month in San Diego.

MilitaryTimes.com on Sunday reported that California-based security firm HALO Corp. will incorporate training to fight the undead during its Oct. 29 to Nov. 2 Counter-Terrorism Summit expected to draw 1,000 military personnel, law enforcement officials, medical experts and government workers to the 44-acre Paradise Point resort island in San Diego’s Mission Bay.

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The company, founded by former special operations, national security and intelligence personnel, says its annual summit this year will include a realistic tactical training environment using “Hollywood magic” in live action demonstrations, realistic tactical training scenarios and classroom education.

Watch the most-viewed videos on NBCNews.com 

Immersive Hollywood sets will include a Middle Eastern village and a pirates’ haven, MilitaryTimes.com reported.

The more than 30 courses range from border and maritime security to cyber terrorism and modern warfare, HALO says in its summit promotional material.

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But a future crisis could arise from an outbreak of viruses that destroy brain cells and render people violently catatonic, like zombies, MilitaryTimes.com said.

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“The Zombie Apocalypse is very whimsical,” Brad Barker, HALO president, told MilitaryTimes.com,  referring to a Centers for Disease Control and Prevention campaign released last year.

Zombies who roam the island will harass the troops, first-aid teams and medical responders participating, Barker told MilitaryTimes.com.

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White House counterterrorism adviser John Brennan on Monday spoke openly -- and at great length -- about what has long been one of the government’s most controversial official secrets:  the use of remotely piloted drones to kill suspected terrorists.

In doing so, he became the first U.S. government official to acknowledge that the drone strikes sometimes kill innocent people, though he characterized such deaths as  “exceedingly rare.” But a new analysis by an independent Washington think tank estimates that more than 300 civilians have been killed by drones since President Barack Obama took office.

In a major speech on the anniversary of Osama bin Laden’s death during a raid in Abbottabad, Pakistan, by U.S. Navy SEALs, Brennan proclaimed that al-Qaida is now "on the path to its destruction."  But the headline was what he had to say about the drone program — long a forbidden subject for senior U.S. officials  — and how the U.S. government uses it.

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“The United States conducts targeted strikes against specific al-Qaida terrorists, sometimes using remotely piloted aircraft, often referred to publicly as drones,” said Brennan, in his speech at the Woodrow Wilson International Center for Scholars, a Washington, D.C., foreign policy think tank.  

While it has been openly reported in the press for years, the use by the CIA of pilotless drones to kill members of al-Qaida has long been officially classified,  prompting government officials to talk obliquely about “lethal operations” and “removal” of terrorists. They have done so even as Obama has dramatically escalated the number of such attacks and made them the central component of the administration’s counterterrorism efforts.

One U.S. intelligence official, speaking on condition of anonymity, told NBC News that the speech represents “a pretty big sea change for us” in terms of what officials will now be permitted to talk about. But the official said that while Brennan’s speech had been carefully vetted throughout the U.S. intelligence and national security community, there had been no formal declassification of the drone program. “The president can declassify anything he wants,” said the official, adding that Brennan – as the representative of the president — can speak about anything his boss wants him to discuss.   

Under Obama, there have been an estimated 250 drone strikes in northwest Pakistan that have killed as many as 2,345 people, according to an analysis by the New America Foundation, a Washington think tank that closely tracks the program. Such strikes have generated a storm of protest in Pakistan and stepped up demands by the Pakistani government to halt them.   

In what he described as an effort to be more open with the American people, Brennan on Monday described an elaborate process under which senior government officials select targets for drone strikes. They must first determine whether a prospective target is a bona fide member of al-Qaida or “associated forces” and poses a “significant threat” to U.S. interests.  The “lethal action” strikes are not used for “punishing terrorists for past crimes” or “seeking vengeance.” Instead, they are used to “stop plots” and “prevent future attacks,” citing as one example, targeting individuals  who possess “unique operational skills.”

Read more reporting by Michael Isikoff in 'The Isikoff Files'

Brennan  said the use of drones gives U.S. intelligence agencies the ability to use “laser-like” precision against the terrorists. But he acknowledged that "innocent civilians have been killed in these strikes." He said such instances have been "exceedingly rare, but it has happened.

“When it does, it pains us and we regret it deeply, as we do any time innocents are killed in war," he added. 

That passage of his speech alone was significant. In June 2011, Brennan said that in the previous year of operations in the government’s then-unspecified program to eliminate al-Qaida members, “There hasn’t been a single collateral death because of the exceptional proficiency, precision of the capabilities we’ve been able to develop.”   

Brennan later changed that statement in response to questions by the New York Times, spurred in part by  reports about a May 6 strike in Pakistan that  hit a religious school, an adjourning restaurant and a house, killing 18 people. Although 12 militants were allegedly killed, British and Pakistani journalists on the scene reported that six civilians also died in the strike.

In Brennan’s adjusted statement last year, he said, “Fortunately, for more than a year, due to our discretion and precision, the U.S. government has not found credible evidence of collateral deaths resulting from U.S. counterterrorism operations outside of Afghanistan or Iraq.”

Brennan did not give any details on Monday about how rare civilian deaths have been. But according to the analysis by the New America Foundation, which relies heavily on local media and other reports from observers in Pakistan, about 17 percent of those who have been killed by drones since the program effectively began in 2004 were “non-militants.”  The foundation estimated that the  “non-military fatality rate” has since dropped to about 13 percent under Obama – as drone strikes have become more frequent and more precise.

Those numbers translate to 471 civilian deaths, including 309 under Obama.

Human rights groups — who have challenged the administration to be more open about its drone program — were not satisfied with the new details provided by Brennan’s speech.

“It is not enough that care is taken to avoid harm to innocent civilians,” said Raha Wala, an official with Human Rights First. “Brennan's assertion that any 'member' of al-Qaida or 'associated forces' is legally targetable is wrong. Under the laws of armed conflict, only members of the enemy's armed forces, or those directly participating in hostilities or who perform a continuous combat function, may be targeted.”

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