“The New York Police Department recommended increasing surveillance of thousands of Shiite Muslims and their mosques, based solely on their religion, as a way to sweep the Northeast for signs of Iranian terrorists,” the Associated Press reported yesterday.

The report is based on interviews and a May 2006 secret NYPD document prepared for Commissioner Raymond Kelly which the AP obtained. The document specifically lists “Shia locations” to monitor in New York and its vicinity, though none of the mosques or organizations listed, the AP notes, have been linked to terrorist organizations.

A former police official who had seen the report told the AP that, “generally, the recommendations were followed but he could not say for sure whether these mosques were infiltrated.” After the document was published yesterday, Kelly said it was a “contingency plan” in the case of a military conflict between the U.S. and Iran.

The document challenges claims made by Mayor Michael Bloomberg that the NYPD never considers religion in its policing. “We don’t stop to think about the religion,” he said in response to a different AP report last August. “We stop to think about the threats and focus our efforts there.”

The AP’s report is the latest in its broad ongoing investigation into the NYPD’s intelligence unit that — in close collaboration with the CIA — developed clandestine spying programs to monitor Muslim communities in New York — without congressional oversight.

In August, the AP first reported that, although the CIA is prohibited from collecting intelligence domestically, a veteran CIA officer (whose name remains classified) on the agency’s payroll was working within the police department. Last week it was announced that the officer would be leaving the NYPD, following an internal CIA inquiry.

The investigation’s revelations about the department’s efforts to monitor the daily lives of Muslims — even those not suspected of wrongdoing and those who were partners in the city’s fight against terror — have raised questions about how the country’s largest police department views Muslims and its relationships with the city’s Muslim communities.

Muslim groups called for Commissioner Kelly’s resignation earlier this month after the Brennan Center for Justice uncovered (PDF) that a controversial documentary about Islam entitled “The Third Jihad” was shown “on a continuous loop” to 1,500 officers during police training back in 2010. Though NYPD spokesperson Paul Browne denied that Kelly had agreed to an interview for the film, it was later revealed that that Browne himself had recommended that Kelly give the interview. The film has provoked outrage among Muslims for its depiction of Islam, and Mayor Bloomberg said the decision to show the film “exercised some terrible judgment.”

In December, 34 members of Congress wrote letters to the Department of Justice (PDF) and the House Judiciary Committee (PDF), calling for investigations into the NYPD’s tactics in surveilling Muslims, citing the AP’s reporting.

This afternoon a coalition of more than 40 New York grassroots organizations and Muslim community groups plans to hold a “rally for justice” in lower Manhattan to call for Commissioner Kelly’s resignation and greater NYPD accountability. A flyer distributed over email for the event states: “The NYPD is watching us, but who is watching the NYPD?”