Police talked with local authorities about professors 300 miles (480 kilometers) away in Buffalo and even sent an undercover agent on a whitewater rafting trip, where he recorded students' names and noted in police intelligence files how many times they prayed.
Detectives trawled Muslim student websites every day and, although professors and students had not been accused of any wrongdoing, their names were recorded in reports prepared for Police Commissioner Raymond Kelly.
"As a result, the NYPD deemed it prudent to get a better handle on what was occurring at MSAs," Browne said in an email. He said police monitored student websites and collected publicly available information, but did so only between 2006 and 2007.
"I see a violation of civil rights here," said Tanweer Haq, chaplain of the Muslim Student Association at Syracuse. "Nobody wants to be on the list of the FBI or the NYPD or whatever. Muslim students want to have their own lives, their own privacy and enjoy the same freedoms and opportunities that everybody else has."
In recent months, the AP has revealed secret programs the NYPD built with help from the CIA to monitor Muslims at the places where they eat, shop and worship. The AP also published details about how police placed undercover officers at Muslim student associations in colleges within the city limits; this revelation has outraged faculty and student groups.
Though the NYPD says it follows the same rules as the FBI, some of the NYPD's activities go beyond what the FBI is allowed to do.
Kelly and New York City Mayor Michael Bloomberg repeatedly have said that the police only follow legitimate leads about suspected criminal activity.
But the latest documents mention no wrongdoing by any students.
In one report, an undercover officer describes accompanying 18 Muslim students from the City College of New York on a whitewater rafting trip in upstate New York on April 21, 2008. The officer noted the names of attendees who were officers of the Muslim Student Association.
"In addition to the regularly scheduled events (Rafting), the group prayed at least four times a day, and much of the conversation was spent discussing Islam and was religious in nature," the report says.
Praying five times a day is one of the core traditions of Islam.
Jawad Rasul, one of the students on the trip, said he was stunned that his name was included in the police report.
"It forces me to look around wherever I am now," Rasul said.
But another student, Ali Ahmed, whom the NYPD said appeared to be in charge of the trip, said he understood the police department's concern.
"I can't blame them for doing their job," Ahmed said. "There's lots of Muslims doing some bad things and it gives a bad name to all of us, so they have to take their due diligence."
City College criticized the surveillance and said it was unaware the NYPD was watching students.
"The City College of New York does not accept or condone any investigation of any student organization based on the political or religious content of its ideas," the college said in a written statement. "Absent specific evidence linking a member of the City College community to criminal activity, we do not condone this kind of investigation."
Browne said undercover officers go wherever people they're investigating go. There is no indication that, in the nearly four years since the report, the NYPD brought charges connecting City College students to terrorism.
Student groups were of particular interest to the NYPD because they attract young Muslim men, a demographic that terrorist groups frequently draw from. Police worried about which Muslim scholars were influencing these students and feared that extracurricular activities such as paintball outings could be used as terrorist training.
The AP first reported in October that the NYPD had placed informants or undercover officers in the Muslim Student Associations at City College, Brooklyn College, Baruch College, Hunter College, City College of New York, Queens College, La Guardia Community College and St. John's University. All of those colleges are within the New York City limits.
A person familiar with the program, who like others insisted on anonymity because he was not authorized to discuss it, said the NYPD also had a student informant at Syracuse.
Police also were interested in the Muslim student group at Rutgers, in New Brunswick, New Jersey. In 2009, undercover NYPD officers had a safe house in an apartment not far from campus. The operation was blown when the building superintendent stumbled upon the safe house and, thinking it was some sort of a terrorist cell, called the police emerency dispatcher.
The FBI responded and determined that monitoring Rutgers students was one of the operation's objectives, current and former federal officials said.
The Rutgers police chief at the time, Rhonda Harris, would not discuss the fallout. In a written statement, university spokesman E.J. Miranda said: "The university was not aware of this at the time and we have nothing to add on this matter."
Another NYPD intelligence report from Jan. 2, 2009, described a trip by three NYPD officers to Buffalo, where they met with a high-ranking member of the Erie County Sheriff's Department and agreed "to develop assets jointly in the Buffalo area, to act as listening posts within the ethnic Somalian community."
The sheriff's department official noted "that there are some Somali Professors and students at SUNY-Buffalo and it would be worthwhile to further analyze that population," the report says.
Browne said the NYPD did not follow that recommendation. A spokesman for the university, John DellaContrada, said the NYPD never contacted the administration. Sheriff's Departments spokeswoman Mary Murray could not immediately confirm the meeting or say whether the proposal went any further.
Another report, entitled "Weekly MSA Report" and dated Nov. 22, 2006, explained that officers from the NYPD's Cyber Intelligence unit visited the websites, blogs and forums of Muslim student associations as a "daily routine."
The universities included Yale; Columbia; the University of Pennsylvania; Syracuse; New York University; Clarkson University; the Newark and New Brunswick campuses of Rutgers; and the State University of New York campuses in Buffalo, Albany, Stony Brook and Potsdam; Queens College, Baruch College, Brooklyn College and La Guardia Community College.
"Students who advertised events or sent emails about regular events should not be worried about a 'terrorism file' being kept on them. NYPD only investigated persons who we had reasonable suspicion to believe might be involved in unlawful activities," Browne said.
But such assurances seem to offer little comfort to some former students.
One University at Buffalo student, Adeela Khan, did end up in a police report after receiving an email on Nov. 9, 2006, announcing an upcoming Islamic conference in Toronto. The email said "highly respected scholars" would be attending, but did not say who or give any details of the program. Khan says she clicked "forward," sent it to a Yahoo chat group of fellow Muslims and promptly forgot about it.
"A couple people had gone the year prior and they said they had a really nice time, so I was just passing the information on forward. That's really all it was," said Khan, who has since graduated.
Khan was a board member of the Muslim Student Association at the University at Buffalo at the time. She says she never went to the conference, was not affiliated with it and had no idea who was speaking at it.
But officer Mahmood Ahmad of the NYPD's Cyber Intelligence Unit took notice and listed Khan in his weekly report for Kelly. The officer began researching the Toronto conference and found that one of the speakers, Tariq Ramadan, had his U.S. visa revoked in 2004. The U.S. government said it was because Ramadan had given money to a Palestinian group. It reinstated his visa in 2010.
The officer's report notes three other speakers. One, Siraj Wahaj, is a prominent but controversial New York imam who has attracted the attention of authorities for years. Prosecutors included his name on a 3 ½-page list of people they said "may be alleged as co-conspirators" in the 1993 World Trade Center bombing, though he was never charged.
The other two are Hamza Yusuf and Zaid Shakir, two of the nation's most prominent Muslim scholars. Both have lectured at top universities in the U.S.. Yusuf met with President George W. Bush at the White House following the 2001 terrorist attacks.
The post about the academic event was enough to get Khan's name mentioned in the weekly MSA report, which was stamped "SECRET" in red letters and sent to Kelly's office.
There is no indication that the investigation went any further, or that Khan was ever implicated in anything. But she worries about being associated with the police report.
"It's just a waste of resources, if you ask me," she said. "I understand why they're doing it, but it's just kind of like a Catch-22. I'm not the one doing anything wrong."
The university said it was unaware its students were being monitored.
"UB does not conduct this kind of surveillance and if asked, UB would not voluntarily cooperate with such a request," the university said in a written statement. "As a public university, UB strongly supports the values of freedom of speech and assembly, freedom of religion, and a reasonable expectation of privacy."
The same Nov. 22, 2006, report also noted seminars announced on the websites of the Muslim student associations at New York University and Rutgers University's campus in Newark, New Jersey.
Browne, the police department spokesman, said intelligence analysts were interested in recruiting by the Islamic Thinkers Society, a New York-based group that wants to see the United States governed under Islamic law. Morton was a leader of the group and went to Stony Brook University's MSA to recruit students that same month.
"One thing that our open source searches were interested in determining at the time was, where do Islamic Thinkers Society go — in terms of MSAs for recruiting," Browne said.
Yale declined comment. The University of Pennsylvania did not immediately respond to requests for comment. Other colleges on the list said they worried the monitoring infringed on students' freedom of speech.
"Like New York City itself, American universities are admired across the globe as places that welcome a diversity of people and viewpoints. So we would obviously be concerned about anything that could chill our essential values of academic freedom or intrude on student privacy," Columbia University spokesman Robert Hornsby said in a written statement.
Danish Munir, an alumnus adviser for the University of Pennsylvania's Muslim Student Association, said he believes police are wasting their time by watching college students.
"What do they expect to find here?" Munir said. "These are all kids coming from rich families or good families, and they're just trying to make a living, have a good career, have a good college experience. It's a futile allocation of resources."
View the report at: http://apne.ws/zLpfdM
Associated Press reporters Matt Apuzzo, Adam Goldman and Eileen Sullivan contributed to this report.