The city Law Department filed a notice of appeal Friday in U.S. District Court in Manhattan.
"We have moved ahead with our formal filings," said Michael A. Cardozo, head of the city Law Department. "The mayor, the police commissioner and the city vowed to press forward immediately with an appeal - and we have done so. The safety of all New Yorkers is at stake."
Lawyers now have about three months to file the formal brief.
Officers have made about 5 million stops in the past decade under the program, mostly of black and Hispanic men. About half are frisked. Only about 10 percent end in arrest and a weapon is recovered a fraction of the time.
A class-action lawsuit argued the department was wrongly targeting minorities and that officers were pressured to make stops by their superiors.
Judge Shira Scheindlin agreed in a lengthy opinion issued Monday, finding that police made street stops based on race. She ordered changes to officer training, discipline and supervision and appointed an outside monitor to supervise and come up with specifics on how the changes will work. She made specific changes to the form the officers fill out when recording a stop, and ordered a yearlong pilot program of body-worn cameras in one precinct per borough where the most stops occur.
Mayor Michael Bloomberg has called ruling unfair and warned that it will damage the NYPD's successes in fighting violent crime.