The woman, who has not been named but who works as an aide to Cuomo, says the three-term governor assaulted her at his executive mansion last year.
Her allegation formed part of an explosive report released this week that said Cuomo sexually harassed 11 former and current state employees.
The veteran Democrat, 63, has repeatedly denied ever touching a woman inappropriately.
“A criminal complaint was filed yesterday,” an official at the Albany County sheriff’s office told AFP.
US media said the complaint was made by a woman referred to as “Executive Assistant #1” in the report made public by New York state Attorney General Letitia James on Tuesday.
The independent investigation, which was civil in nature, said Cuomo had sexually harassed 11 former and current state employees.
“Executive Assistant #1” told the probe that Cuomo put his hand up her blouse in his office in November 2020.
Cuomo’s lawyers hit back at James’s investigation in a press conference Friday.
They complained that they had not received prior notice that the report was about to be released and said the investigators had not shared testimony transcripts with them.
“This was one-sided and he was ambushed,” said Cuomo’s attorney, Rita Glavin.
The lawyer also showed reporters transcripts of emails purportedly sent by Executive Assistant #1 that Glavin said shed doubt on her testimony.
James’s press secretary Fabien Levy responded to the “attack” on the “independence and credibility” of the investigation in a statement Friday, saying, “any suggestion that attempts to undermine the credibility of these women or this investigation is unfortunate.”
Levy underscored that Cuomo had himself requested James oversee an independent investigation in light of the accusations, adding that redacted interview transcripts would be made available to the state assembly.
“There are 11 women whose accounts have been corroborated by a mountain of evidence,” he said.
At least five district attorneys have since opened inquiries into Cuomo’s behavior.
Legal experts have suggested that Cuomo could face forcible touching misdemeanor charges.
James’s report also accused him of presiding over a toxic workplace for women and of taking retaliatory action against at least one of his accusers.
Cuomo has rejected calls from President Joe Biden and other leading Democrats to quit and state lawmakers are moving to impeach him.
He has been given a deadline of August 13 to submit evidence in his defense to their impeachment investigation.
Cuomo was initially praised for his handling of the coronavirus crisis before he was engulfed in accusations that he covered up the scale of deaths in nursing homes.
He is believed to have long coveted winning a fourth term as governor in elections scheduled for November next year, but a poll released Friday suggested he might have trouble winning.
The Quinnipiac University survey found that 70 percent of New York voters questioned thought he should resign, while 55 percent thought he should be charged with a crime.