The 71-year-old stands accused by two dozen dancers of verbal and physical abuse as well as using his power to extort sexual favors.
"I have denied, and continue to deny, that I have engaged in any such misconduct," he wrote in a letter to the board informing them of his retirement, a copy of which was seen by the Times.
"We thank Peter for his tremendous contributions to New York City Ballet as ballet master in chief for over three decades, leading the Company to exceptional artistic heights and accomplishments," board chairman Charles W. Scharf said in a separate statement also obtained by the Times.
Martins, who is Danish, had been under investigation since an anonymous letter detailing several allegations. A group of dancers later came forward to the Times with further allegations dating back to 1983.
A former principal dancer, Martins became a co-leader of the company in 1983 and sole ballet master in chief in 1989.
It was the latest in a wave of misconduct allegations prompted by investigative reports by the Times and the New Yorker into Hollywood producer Harvey Weinstein, who was accused by more than a hundred women of allegations ranging from rape to harassment.
The outpouring has claimed the careers of powerful men in entertainment, politics, and journalism.
High culture has not been immune. The New York Metropolitan Opera's James Levine, who had been its director for 40 years, was removed in December following abuse allegations.
The Montreal Symphony Orchestra likewise removed long-time conductor Charles Dutoit following a complaint by a female musician.
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