The department has agreed to spell out its practices of intelligence gathering and appoint an independent, civilian lawyer to an oversight committee, according to a legal filing of the settlement Thursday.
This comes after the department settled lawsuits accusing the police force of "suspicionless surveillance and investigation" of Muslims.
The original suit, filed in 2013, accused the New York Police Department of violating the Constitution by "singling out and stigmatizing entire communities of New Yorkers based on their religion," according to a statement by the American Civil Liberties Union, which represented the plaintiffs.
The NYPD did not admit to engaging in any improper practices, and the plaintiffs agreed to drop any claim of fault or wrongdoing by the NYPD, according to the settlement.
Under the agreement, the NYPD guidelines will now explicitly include language that advises authorities on practices including: basis for investigations, investigation duration and techniques and protection of constitutional rights.
Guidelines were modified after 9/11
The guidelines, known as Handschu guidelines, were modified following the September 11 attacks in 2001 to give authorities more leeway in investigating potential threats, former NYPD Deputy Commissioner Paul Browne said in 2012.
The Associated Press obtained a report in 2012 that showed Police Department maps of Newark, New Jersey, and photographs of Muslim residences and mosques. Other reports revealed that authorities had tracked websites and on at least one occasion placed an undercover officer among university students.
"For the first time, this watershed settlement puts much needed constraints on law enforcement's discriminatory and unjustified surveillance of Muslims," said Hina Shamsi, ACLU representative and counsel for the plaintiffs.
"At a time of rampant anti-Muslim hysteria and prejudice nationwide, this agreement with the country's largest police force sends a forceful message that bias-based policing is unlawful, harmful and unnecessary."
"We hope the NYPD's reforms help make clear that effective policing can and must be achieved without unconstitutional religious profiling of Muslims or any other communities," she added.
Mayor: NYC Muslims are partners
"New York City's Muslim residents are strong partners in the fight against terrorism, and this settlement represents another important step toward building our relationship with the Muslim community," said Mayor Bill de Blasio. "Our city's counterterrorism forces are the best in the world, and the NYPD will continue working tirelessly to keep our city safe in the fight against terror while respecting our residents' constitutional rights."
John J. Miller, deputy commissioner of intelligence, said that while the language will change, most of the practices now codified have already been in place and are simply being "memorialized" in the guidelines.
One example of the language change in the current guideline for basis for investigation says "allegation or information indicating possibility of unlawful activity," will now be modified to include "inquiry requires an allegation or information that is articulable and factual," according to a release from the NYPD.
NYPD guidelines will also say that authorities must account for "the potential effect on the political or religious activity of individuals, groups or organizations and the potential effect on persons who, although not a target of the investigations, are affected by or subject to the technique," according to the settlement.
Biggest change: Civilian input
The biggest change for the NYPD will be the independent civilian included in already-existing advisory meetings.
The civilian, who must be a lawyer who can pass background checks and will be bound by a confidentiality order, will be appointed by the mayor in consultation with the police commissioner. He or she will serve a five-year-term, according to a news release from the NYPD.
"We have somebody who is independent, who has no dog in that fight, who sits at that table-- and if they are seeing a pattern of untoward activity, it is their job and obligation, to blow the whistle," Miller said.
While the deputy commissioner of intelligence will "retain sole authority over all intelligence investigations and decisions," the appointed, independent outsider has the ability to raise concerns with higher powers in the Police Department and the judicial system if he or she notices patterns or instances of unlawful abuses, according to Miller.