Gay rights advocates welcomed the apology, which they had sought from the NYPD for years.
Police raided the Stonewall, a Greenwich Village tavern, early on June 28, 1969. At the time, homosexuality was criminalized and most gay bars, including the Stonewall, were operated by organized crime.
Patrons of the bar fought back that night and several days thereafter, leading to unprecedented demonstrations for the rights of lesbian, gay, bisexual and transgender (LGBT) people.
Activists memorialized the first anniversary of the Stonewall rebellion with what they called Christopher Street Liberation Day, starting an annual gay pride tradition that is now celebrated around the world.
The NYPD had resisted previous calls to apologize, but Commissioner James O'Neill chose Thursday (local time) to tell a gathering of gay rights advocates that this month's World Pride events in New York for the 50th anniversary of Stonewall marked the right moment.
"What happened should not have happened," O'Neill said. "The actions taken by the NYPD were wrong, plain and simple. The actions and the laws were discriminatory and oppressive, and for that, I apologize."
Organizers expect some 4 million people to visit New York later this month for World Pride. New York's parade will be held on June 30.
James Fallarino, spokesman for the group NYC Pride, said he welcomed O'Neill's apologies.
"He represents the institution, and the institution and their violence against our community is one of the reasons why Pride exists," he said. "It's really important that the institution take responsibility for what happened."
Former Commissioner William Bratton refused to apologize three years ago while acknowledging the raid was a "terrible experience."
"An apology, I don't think so. I don't think that's necessary," Bratton said. "The apology is all that's occurred since then."
Seymour Pine, the retired deputy police inspector who led the raid, apologized in 2004 before a New York Historical Society event, the New York Times reported in Pine's 2010 obituary.
