The disclosures come as the NYPD is fighting off lawsuits accusing it of engaging in racial profiling while combating crime. Earlier this month, a judge ruled that the department's use of the stop-and-frisk tactic was unconstitutional.
The American Civil Liberties Union and two other groups have sued, saying the Muslim spying programs are unconstitutional and make Muslims afraid to practice their faith without police scrutiny.
Both Mayor Mike Bloomberg and Police Commissioner Raymond Kelly have denied those accusations. They say police do not unfairly target people; they only follow leads.
"As a matter of department policy, undercover officers and confidential informants do not enter a mosque unless they are following up on a lead," Kelly wrote recently in The Wall Street Journal. "We have a responsibility to protect New Yorkers from violent crime or another terrorist attack — and we uphold the law in doing so."
An NPYD spokesman declined to comment.
The NYPD did not limit its operations to collecting information on those who attended the mosques or led prayers. The department sought also to put people on the boards of New York's Islamic institutions to fill intelligence gaps.
One confidential NYPD document shows police wanted to put informants in leadership positions at mosques and other organizations, including the Arab American Association of New York in Brooklyn, a secular social-service organization.
Linda Sarsour, the executive director, said her group helps new immigrants adjust to life in the U.S. It was not clear whether the department was successful in its plans.
The document, which appears to have been created around 2009, was prepared for Kelly and distributed to the NYPD's debriefing unit, which helped identify possible informants.
Around that time, Kelly was handing out medals to the Arab American Association's soccer team, Brooklyn United, smiling and congratulating its players for winning the NYPD's soccer league.