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Protesters called on Police Commissioner Ray Kelly and top aide Paul Browne to resign over the department's surveillance of specific mosques and community centers.

They're also angry over Kelly's involvement in the controversial film "The Third Jihad," which was shown at a police training facility.

"We’re really trying to pick up the pieces of trust here. This has been a breakdown of a relationship between the Muslim community and NYPD, and it’s very clear that this is a renegade police department that needs oversight,” said Cyrus McGoldrick of the New York chapter of the Council on American-Islamic Relations.

“We find out that they're showing this horrible video about Muslims, ‘The Third Jihad,’ and all these wrong stereotypes and hateful propaganda, so we really need to speak out against it, that's why we're here today," said protester Aber Kawas.

The NYPD has apologized for its relationship with the film.

In a statement, Browne said the NYPD continues to work closely with the city's Muslim communities, citing, among other things, the creation of the department's youth cricket and soccer leagues.

Meanwhile, 33 civil rights groups from around the country sent a letter Friday to State Attorney General Eric Schneiderman asking for an investigation into the department.