De Blasio confirmed that he received Barbot's resignation letter before noon Tuesday, and appointed Dr. Dave A. Choksi as her replacement.
The New York Times first reported that Barbot submitted her resignation to de Blasio, amid a clash between the mayor and the city’s health officials.
"I leave my post today with deep disappointment that during the most critical public health crisis in our lifetime, that the Health Department's incomparable disease control expertise was not used to the degree it could have been," she wrote to de Blasio.
"Our experts are world renowned for their epidemiology, surveillance and response work," she continued. "The city would be well served by having them at the strategic center of the response not in the background."
New York health officials have clashed with de Blasio over his decision to take the Health Department’s responsibility for COVID-19 contact tracing and, instead, giving that responsibility to the public hospital system, the Times reported.
Barbot, in a letter to Department of Health colleagues, confirmed her resignation.
"This morning I submitted my formal resignation to Mayor de Blasio," she wrote. "Your experience and guidance have been the beacon leading this city through this historic pandemic and that to successfully brace against the inevitable second wave, your talents must be better leveraged alongside that of our sister agencies."
"I have every confidence that you, the committed individuals of this agency, will continue to dedicate yourselves to protecting the health of all New Yorkers during this unprecedented public health emergency," she added. "The moment demands it without distractions."
Barbot’s resignation came weeks after reports that she made derogatory comments to an NYPD official while receiving requests for masks to protect the police force from COVID-19.
Barbot, in May, addressed the reports that she blew off a request from the NYPD for hundreds of thousands of surgical masks amid the coronavirus pandemic, and reportedly told a high-ranking police official that: “I don’t give two rats’ a--es about your cops.”
“The members of the NYPD fight valiantly every day to keep New Yorkers safe,” Barbot said in a statement Monday.
“In mid-March, I was asked to provide the NYPD with a half million N-95 masks, while masks and other PPE were in terribly short supply,” she explained. “I wished we had sufficient numbers to meet their full request and were ultimately able to partially fulfill what was sought. This regrettably led to an argument in which words were exchanged between a police official and myself.”
She added: “I apologized to that police official then and today, I apologize to the NYPD for leaving any impression whatsoever that I don’t have utmost respect for our police department, which plays a critical role on the frontlines each and every day to keep our city safe.”
Barbot’s apology came after de Blasio publicly called for her to apologize to the NYPD, and after current and former NYPD officers called for her resignation.
The New York Post first reported that Barbot made the remark during a brief phone conversation in March with NYPD Chief of Department Terence Monahan, after he requested 500,000 masks.
Barbot reportedly told Monahan that she could only provide 50,000 masks.
“I don’t give two rats’ a--es about your cops,” Barbot reportedly said. “I need them for others.”
Meanwhile, Barbot’s criticism of de Blasio’s handling of COVID-19 comes as the city recovers from its status as the early epicenter of the coronavirus pandemic.
As of Tuesday, New York City reported more than 231,000 positive cases of COVID-19 and more than 23,000 deaths.