NEW YORK — The New York Police Department compiled lists of mosques and Muslim businesses it saw as potential security risks for reasons that included endorsing conservative religious views or having devout customers, according to hundreds of pages of internal police documents newly obtained by The Associated Press.

The records reveal the extent of an undercover effort that initially studied more than 250 mosques in New York and New Jersey and identified hundreds more “hot spots” in a hunt for terrorists. Many showed obvious signs of criminal behavior, but the police explanations for targeting others were less clear.

A Bangladeshi restaurant, for instance, was identified as a hot spot for having a “devout crowd.” The restaurant was noted for being a “popular meeting location for political activities.”

The documents obtained by the AP, many of which were marked secret, paint the clearest picture yet of how the past decade’s hunt for terrorists also put huge numbers of innocent people under scrutiny as they went about their daily lives in mosques, restaurants and social groups. Every day, undercover officers and informants filed reports from their positions as “listening posts” inside Muslim communities.

At the White House, where President Barack Obama recently urged local authorities not to cast suspicion on entire communities, spokesman Jay Carney declined to comment Tuesday on whether it endorsed the tactics outlined in the NYPD documents.

An AP investigation last month revealed that the department maintains a list of “ancestries of interest” that it uses to focus its clandestine efforts. A secret team known as the Demographics Unit then dispatched plainclothes officers into the community to eavesdrop in cafes and chat up business owners.

That effort has benefited from federal money and an unusually close relationship with the CIA, one that at times blurred the lines between domestic and foreign intelligence-gathering.

After identifying more than 250 area mosques, police officials determined the “ethnic orientation, leadership and group affiliations,” according to the 2006 police documents. Police also used informants and teams of plainclothes officers, known as rakers, to identify mosques requiring further scrutiny, according to an official involved in that effort, who spoke on condition of anonymity because he was not authorized to discuss the program.

Armed with that information, police then identified 53 “mosques of concern” and placed undercover officers and informants there, the documents show.

Many of those mosques were flagged for allegations of criminal activity, such as alien smuggling, financing Hamas or money laundering. Others were identified for having ties to Salafism, a hardline movement preaching a strict version of Islamic law. Still others were identified for what the documents refer to as “rhetoric.”

Other reasons are less clear.

Two mosques, for instance, were flagged for having ties to Al-Azhar, the 1,000-year-old Egyptian mosque that is the pre-eminent institute of Islamic learning in the Sunni Muslim world. Al-Azhar was one of the first religious institutions to condemn the 2001 terrorist attacks. President George W. Bush’s close adviser, Karen Hughes, visited Al-Azhar in 2005 and applauded its courage.

Al-Azhar was also a sponsor of Obama’s 2009 speech reaching out to the Muslim world.

The list of mosques where undercover agents or informants operated includes ones that Police Commissioner Ray Kelly has visited and that area officials have mentioned as part of the region’s strong ties to the Muslim community. Mayor Michael Bloomberg has stood beside leaders of some mosques on the list as allies in fighting terrorism.

The documents are a series of internal presentations, including one prepared for Kelly. Following the AP’s reporting, they were provided to the AP and veteran New York police reporter Leonard Levitt, who runs the website NYPDConfidential.com. Because the list of mosques is so long and explanation for the surveillance is so limited, the AP is not identifying the individual mosques that were under surveillance.

An NYPD spokesman did return messages seeking comment Monday, a holiday, and again Tuesday. The police department has said it follows leads and does not trawl entire neighborhoods.

New York police identified 263 “hot spots” throughout the city, the documents show. Like the mosques, the examples of hot spots ranged from businesses that sold untaxed cigarettes and where inflammatory rhetoric was overheard to those with less obvious criminal connections.

The example of the Bangladeshi restaurant flagged for its “devout” clientele further undercuts Bloomberg’s claim that the NYPD does not take religion into account in its policing. Last week the AP revealed that the NYPD maintained a list of “ancestries of interest” that included “American Black Muslim,” which is a religion, not an ancestry.

Police also kept tabs on seven of the area’s Muslim student associations, defined in the documents as “a university-based student group, with an Islamic focus, involved with religious and political activities.” Two were flagged for having Salafi speakers. One was cited for having students who are “politically active and are radicalizing.”

Since the AP reports, several Muslim civil rights groups and a New York congresswoman have urged the Justice Department to investigate the NYPD for what critics see as racial profiling. Under U.S. Attorney General Eric Holder, the Justice Department has stepped up investigations of local police departments for possible civil rights violations, but none involves national security cases. 

Adam Goldman (AP)