Police say they were worried about certain Muslim scholars who influence students and feared extracurricular activities such as paintball outings could be used as terrorist training.
The AP first reported in October 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.
A source close to 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.
The AP investigation found undercover officers allegedly talked with local authorities about professors 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, according to the Huffington Post.
The New York Police Department defended its surveillance of Muslim student associations in educational institutions hundreds of miles from the city as well as more than 250 mosques in the metropolitan area.
The NYPD says it wanted to get a better handle on what was occurring at the student associations, citing 12 arrests or convictions of people on terrorism charges throughout the United States and abroad who were once members of Muslim student associations.
Both New York City Police Commissioner Raymond Kelly and New York City Mayor Michael Bloomberg say police follow only legitimate leads about suspected criminal activity.
Several New York Democratic state senators have also called for the state attorney general to investigate the NYPD's spying on Muslim neighborhoods.
Just last month, the CIA announced an inspector general investigation into the agency's partnership with the NYPD.
A small number of Capitol Hill and New York lawmakers have called for greater oversight and controls over the police department's intelligence unit.
There is extensive federal oversight of investigations by the FBI and CIA, however, it is not typically the case with the NYPD's counterterrorism unit.