The NYPD’s intelligence bureau routinely violates court-mandated rules meant to safeguard constitutionally protected rights of political or religious targets, according to findings released Tuesday by the department’s independent overseer.

The 64-page report, by Inspector General Philip K. Eure, found that more than half the time the NYPD continued probes even though the required legal permission had expired, and that a quarter of the time such lapses persisted for more than 31 days. More than 95 percent of investigations reviewed by Eure’s team dealt with Muslims, according to the report, which also found that the NYPD did not adequately document the roles of secret informants and undercover officers.

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

The report, based on a random selection of files, concluded that investigators met the legal threshold to open the probes but “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’s top lawyer, Lawrence Byrne, said the department is “pleased” with the report’s findings that the rationales put forth by the NYPD met legal thresholds for beginning probes. The findings reflected only “really a technical, administrative error,” Byrne said Tuesday afternoon at the NYPD’s headquarters in Manhattan.

“We believe we’ve adhered to the letter and the spirit of the law in each instance,” he said.

The Handschu guidelines, as the rules governing NYPD investigations of political activity are known, stem from a decades-old class-action lawsuit that resulted in a 1985 consent decree. The rules were relaxed soon after 9/11 when the NYPD told the judge overseeing the suit that looser standards were needed to protect New York City from terrorism.

Eure found that despite rules requiring specifics in applications to deploy an undercover officer or informant, the NYPD “almost never” did so, “instead repeatedly using generic, boilerplate text” that included the same typographical error in paperwork dating back over a decade. 

John Miller, the NYPD’s deputy commissioner for counterterrorism and intelligence, defended the high number of investigations involving Muslims.

“If you’re investigating al-Qaida, and TTP and ISIL plots against New York City,” Miller said, “your investigative targets are gonna be who they are.”

Earlier this year, the NYPD moved to settle two lawsuits by agreeing to appoint an independent civilian to monitor how the NYPD conducts counterterrorism, among other changes.

Donna Lieberman, the New York Civil Liberties Union executive director whose group is involved in the litigation, said Eure’s findings underscore the “need to rein in NYPD surveillance of American Muslims.”

“The inspector general’s report has provided yet more evidence that the NYPD’s surveillance of American Muslims was highly irregular, operated in a black box and violated even the weaker rules that existed before our proposed settlement,” she said.

The settlement announced earlier this year restores some of the protections that were relaxed post 9/11.