The New York City Police Department routinely violated court-mandated rules on handling investigations of political activity, particularly Muslim groups or individuals, the department's watchdog says in a report.

The 64-page report, released on Tuesday by the Office of the Inspector General for the NYPD, found police were non-compliant with a number of rules governing the conduct of probes, including routinely extending investigations after their legal authorisation expired before seeking renewals.

The examination also showed that police used confidential informants without proper documentation.

The report said 95 percent of police investigations governed by the guidelines involved individuals or political activities predominantly associated with Islam. The report said it investigated cases closed between 2010 and 2015.

The report was intended to measure the department's compliance with a longstanding set of rules, known as the "Handschu" guidelines, first imposed on the NYPD decades ago as part of a federal court settlement.

"These failures cannot be dismissed or minimised as paperwork or administrative errors," the report said. "The very reason these rules were established was to mandate rigorous internal controls to ensure that investigations of political activity - which allow NYPD to intrude into the public and private aspects of people's lives - were limited in time and scope and to ensure that constitutional rights were not threatened."

The regulations were relaxed following the attacks of September 11, 2001, to allow police to expand counter-terrorism and intelligence efforts.

Earlier this year, the city agreed to settle a lawsuit that claimed a secretive NYPD programme which conducted broad surveillance of Muslim neighbourhoods, mosques and businesses violated the Handschu guidelines. The unit that oversaw those investigations was disbanded in 2014 after Mayor Bill de Blasio took office.

At a news conference on Tuesday, police officials characterised the violations as technical and administrative errors, not a failure to renew expired cases.

John Miller, the department's top counterterrorism official, said working within the guidelines of the law is necessary to stop terrorist groups.

"If you're investigating al-Qaeda, and TTP and ISIL plots against New York City, your investigating targets are going to be who they are," Miller said, referring to the Pakistan Taliban and Islamic State.

This summer, the NYPD activated an electronic case tracking system dedicated to all Handschu investigations that automatically tracks renewed dates and authorisations, according to police documents.

"We take our Handschu responsibility very seriously," said Lawrence Byrne, the department's deputy commissioner for legal matters.

"There was no violation of the Handschu laws."