The violent police raid at the Stonewall Inn in New York City in 1969 is widely regarded as a seminal event in the gay rights movement. But police officials had long refused to admit that officers’ behavior and the raid itself were not justified, leaving a rift between law enforcement and gay-rights supporters that seemed to deepen distrust over the years.

On Thursday, as people around the world began commemorating the 50th anniversary of the clash, New York’s police commissioner took a step toward making amends, issuing an unusual official apology on behalf of the Police Department for the actions of officers during the Stonewall uprising.

“The actions taken by the N.Y.P.D. were wrong — plain and simple,” the commissioner, James P. O’Neill, said during an event at Police Headquarters.

It was an admission that gay rights leaders said was momentous and unexpected, if overdue.

“To have the N.Y.P.D. commissioner make these very explicit remarks apologizing, it’s really moving,” said Corey Johnson, the City Council speaker, who is gay and who had a day earlier called for a police apology.

Still, some cautioned the Police Department that its future actions needed to back up its words.

“The history of police violence and criminalization of L.G.B.T.Q. people sadly continues to this day,” said Richard Saenz, an attorney at Lambda Legal, a national civil rights organization.