The NYPD confirmed the probe following a "60 Minutes" broadcast Sunday night in which an unnamed woman accused Batali of drugging and sexually assaulting her in 2005.
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She said she remembers joining him for a glass of wine at a Manhattan restaurant, then waking up on the floor feeling drugged and assaulted. She also said she talked to the police, but never filed a report.
Batali issued a statement to CBS denying that he assaulted the woman. He sent this statement to ABC News on Monday:
"I vehemently deny any allegations of sexual assault. My past behavior has been deeply inappropriate and I am sincerely remorseful for my actions. I am not attempting a professional comeback. My only focus is finding a personal path forward where I can continue in my charitable endeavors - helping the underprivileged and those in need."
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The celebrity chef stepped down from daily operations at his restaurant empire and ABC cooking show "The Chew" in December after four women accused him of inappropriate touching over a period of 20 years. Batali has apologized for those encounters.
The restaurant group co-owned by Batali said it has been "actively negotiating" to buy him out.
"Mr. Batali has had no direct involvement with Eataly since December 2017," a spokesperson for the food hall said in an emailed statement. "We have initiated a process to compel the divestiture of his small, minority interest in Eataly USA."
The B&B Hospitality Group said Batali and his partner, Joe Bastianich, have signed a letter of intent and final terms could be set by July 1.
B&B said it had been unaware of what it calls the "chilling" and "deeply disturbing" allegations.
ABC News contributed to this report.