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The NYPD’s counter-terror cops spied on its subjects even after surveillance deadlines expired, according to a new report by the department’s Inspector General.

In more than half the cases closed by the Intelligence Bureau between 2010 and 2015 that were randomly reviewed by the Inspector General’s office, the NYPD failed to properly renew investigations before the legally granted permission to surveil subjects had expired.

Yet the department continued spying on subjects — the vast majority of whom were affiliated with the Muslim faith — even after their surveillance powers had lapsed.

In more than 25 percent of the surveillance cases reviewed, the deadlines had lapsed by more than a month before being properly renewed.

“This investigation demonstrates a failure by NYPD to follow rules governing the timing and authorizations of surveillance of political activity,” said Mark Peters, commissioner of the city’s Department of Investigation.

Larry Byrne, head of the NYPD’s Legal Affairs Bureau, noted that all of the investigations were for valid purposes.

“The most important finding the IG made was that every one of our investigations and that every one of the people we investigated were investigated for valid and proper purposes,” said Byrne.

“We’ve very pleased with that finding.”

The report also found that the NYPD failed to renew approval for confidential informants and undercover officers used in investigations more than 57 percent of the time.

Investigators regularly failed to adequately document what role those sources played in the scope of the investigation.

Despite the violation, the IG’s office found no ill-intent.

“While we found no evidence of improper motives, these rules are important to protect the rights of all New Yorkers and must be rigorously followed,” Peters said.

The NYPD is required to follow the guidelines laid out in the Handschu Agreement — which came after a 1985 court settlement and governs into investigations that may involve a person’s “political activity.”

But the rules were relaxed after the attacks of September 11, 2001, which led to the creation of the NYPD’s Demographics Unit, which was intended to gain intel by covertly spying on people and place in the city’s Muslim enclaves.

That unit was disbanded in 2014 when the department determined it to be unproductive — and cries from the Muslim community who were opposed to what they felt was gratuitous spying.

The IG said adherence to the rules would not hinder the NYPD’s anti-terrorism efforts.

“When investigating political activity, however, NYPD must adhere to well-established rules governing how these investigations can be opened and extended,” said Philip Eure, the NYPD’s Inspector General.

“Our recommendations, if implemented, will ensure tighter compliance with these rules in a way that will promote greater police accountability and give the public greater confidence in how NYPD operates.”

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