NEW YORK (AP) — The New York City Police Department likely turned a blind eye to violations of the constitutional rights of thousands of individuals detained at private residential buildings in the Bronx in a stop-and-frisk program that’s under assault in the courts, a federal judge said Tuesday.

U.S. District Judge Shira Scheindlin said the department’s “Operation Clean Halls” program — aimed at preventing illegal activity at buildings in high-crime areas — had apparently stopped people who were merely entering or exiting buildings and not acting suspicious.

Officers can continue to make stops under the program and Scheindlin ordered the department to develop and adopt a written policy describing limited circumstances when a person on a suspicion of trespass can be stopped. She also ordered the department to revise its training materials and programs to conform with the law, though she suspended the effect of these orders until the city can challenge them legally in coming weeks.

Scheindlin said the plaintiffs who presented evidence at a fall hearing had shown a clear likelihood of proving the city had shown deliberate indifference toward a widespread practice of unconstitutional trespass stops by police outside the buildings.

“While it may be difficult to say where, precisely, to draw the line between constitutional and unconstitutional police encounters, such a line exists, and the NYPD has systematically crossed it when making trespass stops” outside Bronx buildings, she said.

Scheindlin said she was not ordering the abolition or even a reduction of the program because it appears to be a valuable way to use police resources to enhance security in private buildings.

But police Commissioner Raymond Kelly said the ruling “unnecessarily interferes with the department’s efforts to use all of the crime-fighting tools necessary to keep Clean Halls buildings safe and secure.”

He noted landlords had requested extra police protection, and he compared it to Manhattan doormen “who routinely challenge visitors to their apartment buildings.

“Through ‘Clean Halls,’ the police have worked to provide a modicum of safety for less prosperous tenants,” Kelly said.

City Corporation Counsel Michael A. Cardozo said there was no basis for federal court intervention and that remedial steps the judge proposed would place an unacceptable burden on the police department to adopt additional training, supervision, monitoring and reporting requirements.

Donna Lieberman, executive director of the New York Civil Liberties Union, called the ruling “a major step toward dismantling the NYPD’s stop-and-frisk regime.” She said Operation Clean Halls “has placed New Yorkers, mostly black and Latinos, under siege in their own homes in thousands of apartment buildings.”

The rulings came in a lawsuit brought by black and Latino residents who said police have a widespread practice of making unlawful stops on suspicion of trespass outside Bronx buildings. The ruling is an interim order before a trial on the lawsuit. The judge said her remedial proposals also will apply to another lawsuit that more broadly challenges stop-and-frisk practices.

McGregor Smyth of The Bronx Defenders, who worked on the case, said Operation Clean Halls has existed in some form since 1991. He said nearly every private apartment building in some Bronx neighborhoods is enrolled, leaving 3,261 buildings participating in the Bronx and 8,032 citywide. He said the program lets officers conduct regular floor-by-floor sweeps and engage in particularly aggressive stop, question, frisk and arrest practices.

It is not enough for a police officer to have a non-specific suspicion or hunch about a person to perform a stop and frisk, Scheindlin said. The plaintiffs have said the stops left them feeling violated, disrespected, angry and defenseless, she noted.

“The evidence of numerous unlawful stops at the hearing strengthens the conclusion that the NYPD’s inaccurate training has taught officers the following lesson: stop and question first, develop suspicions later,” Scheindlin said.

She said she was not ordering the abolition or even a reduction of the program because it appears to be a valuable way to use police resources to enhance security in private buildings.

The case Scheindlin ruled on is the narrowest of three challenging stop-and-frisk policies. It deals with legal issues raised after the city first adopted a stop and frisk law in 1964 that allows police to stop, question and sometimes frisk people they think might be doing something criminal, even if officers’ suspicions don’t meet the probable-cause standard for an arrest.