As alarm mounted this year over conditions at the Rikers Island jail complex, the administration of Mayor Bill de Blasio largely managed to escape scrutiny, because the problems were rooted in its predecessor.

But on Monday, the top federal prosecutor in Manhattan criticized the de Blasio administration for the first time, suggesting that New York officials were not moving quickly enough to make reforms at Rikers and warning that his office stood ready to file a civil rights lawsuit against the city to force changes. He referred to an article in The New York Times, which revealed that key portions of a report on violence at Rikers had been withheld from federal investigators and that officials involved in reporting distorted data were promoted.

“If, as has been reported, incomplete and inaccurate information has been provided to us, and questionable promotions may have occurred, it does not instill confidence in us that the city will quickly meet its constitutional obligations,” the prosecutor, Preet Bharara, the United States attorney for the Southern District of New York, said.

Mr. Bharara’s office has been in discussions with the mayor’s office since publishing the findings on Aug. 4 of a lengthy civil rights investigation into the abuse of teenage inmates at Rikers. The investigation yielded a scathing 79-page report that included more than 10 pages of recommendations, and said the city had 49 days — a period that ended on Monday — to agree to “develop specific policies and procedures that will implement the remedial measures” or potentially face a lawsuit.