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The New York Police Department has entered a settlement agreement on Thursday after being sued by civil right groups for illegal surveillance of Muslims in New York.

Under the terms of a settlement, the NYPD will strengthen safeguards against illegal surveillance of Muslims in investigations of terror threats and install a civilian representative on an advisory committee that reviews the probes.

The announcement of a deal following months of negotiations formally ended litigation over accusations that the largest police department in the US cast a shadow over Muslim communities with a covert campaign of religious profiling and illegal spying.

"We are committed to strengthening the relationship between our administration and communities of faith so that residents of every background feel respected and protected," Mayor Bill de Blasio said in a statement.

The suits were among legal actions that followed reports that revealed how city police infiltrated Muslim student groups, put informants in mosques and otherwise spied on Muslims as part of a broad effort to prevent terrorist attacks.

The settlement modifies and adds restrictions on surveillance set by the court-ordered Handschu decree, which was put in place in response to surveillance used against war protesters in the 1960s and '70s.

This settlement is important in light of escalating anti-Muslim rhetoric and hate crimes in the US, but at the same time we hope Mayor de Blasio will be more vocal about why the department was simply wrong to engage in religious profiling of the Muslim community in the first place. - Center for Constitutional Rights

The decree was relaxed following the 11 September 2001 terror attacks to allow police to more freely monitor political activity in public places.

Civil rights groups sued in 2013 in federal court in Manhattan, accusing the NYPD of breaking Handschu rules. A second suit filed that year in Brooklyn federal court by mosques, a charity and community leaders alleged that the department was discriminating against Muslims.

The city had begun settlement talks last year, and a tentative deal in the Brooklyn case had been reached in June.

Although it doesn't require the NYPD to admit any wrongdoing or the city to pay monetary damages, the agreement "will curtail practices that wrongly stigmatise individuals" while making investigations "more effective by focusing on criminal behavior," said Arthur Eisenberg, legal director for the New York Civil Liberties Union.

Under the deal, the Handschu guidelines will specifically ban investigations based on race, religion or ethnicity.

Other provisions require the department to try to use the least intrusive investigative techniques possible and to consider "the potential effect on the political or religious activity of individuals, groups or organisations and the potential effect on persons who, although not a target of the investigation are affected by or subject to the technique."

Another provision requires the NYPD to remove from a department website a 2007 report warning of a "radicalisation" process that puts young Middle Eastern immigrants on a path to commit acts of homegrown terrorism.

Muslim groups had called the findings faulty and inflammatory.

"This settlement is important in light of escalating anti-Muslim rhetoric and hate crimes in the US, but at the same time we hope Mayor de Blasio will be more vocal about why the department was simply wrong to engage in religious profiling of the Muslim community in the first place," the Center for Constitutional Rights said in a statement.