New York (CNN) -- While New York police officials defended their actions, Muslim advocacy groups Friday expressed disappointment that the state's attorney general declined to investigate the department over alleged surveillance of Muslim neighborhoods.
New York Attorney General Eric Schneiderman earlier this month received a letter from 33 civil liberties and civic organizations.
"While we share some of the serious concerns raised in the letter, there are significant legal and investigative obstacles that impede our ability to launch a review of the matter at this time," said attorney general spokesman Danny Kanner.
The coalition of advocacy groups decried Schneiderman's decision, saying it hoped the official "would have had the moral courage to do the right thing and uphold the civil rights of Muslim New Yorkers, many of whom have been spied on by their police force simply because of their faith, not based on any wrongdoing." It urged Schneiderman to reconsider his decision.
New York Police Commissioner Raymond Kelly told reporters Friday "we're doing what we have to do to protect the city."
"I've received some letters asking some questions," Kelly said. "I also receive letters of support, so there's not one consistent opinon if you will. I think we have a good working relationship with the Muslim community in the city."
Complaints also extend to NYPD surveillance in Muslim neighborhoods in Newark, New Jersey.
"We have to be cognizant of what's going on in the surrounding area," the commissioner said. "It would be naive of us to limit our focus to the five boroughs of New York City." Bombs or components built for attacks have been built in New Jersey and Connecticut, he said.
The mayor of Newark has called for an investigation.
"The Newark Police Department was not involved in joint operations with the New York Police Department as was described in the disclosed NYPD report," Mayor Cory Booker said Wednesday, referring to a leaked internal New York police document that allegedly detailed police surveillance of Muslim-owned business and mosques across the city.
"I strongly believe that we must be vigilant in protecting our citizens from crime and terrorism, but to put large segments of a religious community under surveillance with no legitimate cause or provocation clearly crosses a line," he said.
But New York police say their Newark counterparts were "briefed before and afterwards, and a Newark liaison officer accompanied NYPD personnel when they were in Newark," according to a statement from NYPD spokesman Paul Browne.
"We're following leads, wherever those leads take us," Kelly said.
The 60-page report, obtained by The Associated Press, showed maps of Newark and photographs of Muslim residences and mosques. There was no statement in the document regarding terrorism or criminal activity.
New York University 's president sent a letter to Kelly, saying that if police were targeting Muslims based on religion alone, that he found that "troubling and problematic."
New York Mayor Michael Bloomberg has defended the extent of police surveillance against critics who have suggested that authorities went too far. And Kelly said he didn't believe civil liberties were trampled.
"We have to keep this country safe," the mayor told reporters, addressing questions about a separate report, also leaked to AP, that indicated New York police were closely monitoring Muslim student associations in schools across the Northeast.
"If people put things on websites and make them available to everybody, of course the NYPD is going to look at anything that's publicly available in the public domain," Bloomberg said. "And given we've had a dozen people arrested or convicted of terrorist acts who've come from similar organizations, we have an obligation to do so."
That report said police have tracked websites, and on one occasion sent an undercover officer with students from the City College of New York on a whitewater rafting trip in 2008.
A law enforcement official said intelligence gathering had indicated that an extremist group, commonly known as Al Muhajiroun, was suspected of having a possible connection to students at the City College of New York.
Police then sent an undercover agent to monitor Muslim students on campus for signs of criminal behavior. The official says that action was cleared by authorities beforehand so as to adhere to legal requirements, and that the decision was approved by a NYPD legal panel.
That panel included a NYPD attorney, as well as a civilian lawyer appointed by the mayor, the official said. CNN cannot independently confirm those accounts.
During the rafting trip, the undercover agent found no suspicious activity, the official said.
Al Muhajiroun, which is thought to have been based in the United Kingdom, operates under different names and remains a focus of counterterrorism efforts.
The group has also spawned splinter factions, including the Revolution Muslim and The Islamic Thinkers Society, and is thought to have disseminated extremist ideas among Muslim youth in the United States, according to CNN terrorism analyst Paul Cruickshank.
When a reporter asked if police had gone too far by sending the agent on the rafting trip, Bloomberg responded, "No."
Police told CNN earlier that officers do not track students directly, but confirmed that they monitor websites the students use.
In 2006, the police program concerning the monitoring of websites was canceled only six months after it began after the probe failed to yield information pertinent to law enforcement, according to a senior law enforcement official.
CNN's Susan Candiotti and Mary Snow contributed to this report.