New York City’s health commissioner, Dr. Oxiris Barbot, resigned on Tuesday to protest her “deep disappointment” with Mayor Bill de Blasio’s handling of the coronavirus outbreak, renewing scrutiny of his overall leadership during the crisis.

Her departure came after escalating tensions between City Hall and top city health department officials, which had begun at the start of the outbreak in March, burst into public view and raised concerns that the feuding was undermining crucial public health policies.

“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,” Dr. Barbot said in her resignation email sent to Mr. de Blasio, a copy of which was shared with The New York Times.

“Our experts are world renowned for their epidemiology, surveillance and response work. The city would be well served by having them at the strategic center of the response not in the background.”

Mr. de Blasio reacted to her resignation by defending his handling of the outbreak, which devastated the city in the spring, killing more than 20,000 residents, even as it has largely subsided in recent weeks. On Monday, 316 people tested positive out of the just over 30,000 tested.

Still, the turnover in the Department of Health and Mental Hygiene comes at a pivotal moment: Public schools are scheduled to partially open next month — which could be crucial for the city’s recovery — and fears are growing that the outbreak could surge again when the weather cools.

“It had been clear in recent days that it was time for a change,” Mr. de Blasio said in a hastily called news conference. “We need an atmosphere of unity. We need an atmosphere of common purpose.”

The mayor moved quickly to replace Dr. Barbot, immediately announcing the appointment of a new health commissioner, Dr. Dave A. Chokshi, a former senior leader at Health + Hospitals, the city’s public hospital system.

At no point in the statement about Dr. Chokshi’s appointment did the mayor thank — or even mention — Dr. Barbot, who had served in his administration since the start of his first term in 2014. Mr. de Blasio did acknowledge her service during the news conference.

The speed of the appointment and the robustness of the announcement — Mr. de Blasio had lined up a former surgeon general to speak highly of Dr. Chokshi — suggested that Dr. Barbot’s resignation had not occurred in a vacuum. One city official said she had done so on Tuesday because she believed she was going to be fired.

“It’s a bad day for the city. She’s a very qualified commissioner of health,” said Lilliam Barrios-Paoli, a former deputy mayor of health under Mr. de Blasio who worked with Dr. Barbot. “There’s another woman of color that goes down. I think it’s a really regrettable thing.

“This is not a position you can put anybody just because. It’s the premier public health agency in the country,” Ms. Barrios-Paoli added. “It’s just a shame that she did not feel that she was supported by the mayor.”

Current and former health officials said the departure of Dr. Barbot reflected Mr. de Blasio’s history of distrust in his health department. From early in the coronavirus outbreak, he has clashed with the department on testing, public messaging and how quickly to shutter schools.

Mr. de Blasio has been faulted for resisting calls to close down schools and businesses, which some epidemiologists believe worsened the outbreak.

Once he decided on closures, Mr. de Blasio pushed for the state to authorize further restrictions, a move ultimately made by Gov. Andrew M. Cuomo. And in the intervening months, the mayor has moved cautiously in reopening the city, guarding the progress that has been made in controlling the virus.

But even as the outbreak began to ebb in late May, tensions with Dr. Barbot mounted.

Some public health officials had bristled at the mayor’s decision to place the city’s contact-tracing program inside Health + Hospitals. The health department has performed such tracing for decades; the public hospitals have not.

Dr. Barbot disagreed with the move, but kept her disapproval private. She nonetheless made fewer public appearances as Mr. de Blasio seemed to look elsewhere for public health guidance, turning to a new senior adviser, Dr. Jay Varma, and to the public hospitals chief, Dr. Mitchell Katz.

On Tuesday, Mr. de Blasio suggested that Dr. Barbot had not been a team player.

“It’s never about one agency,” he said at one point. He used the words “teamwork” or “team” 15 times in a 38-minute news conference.

New York City’s health department is regarded as one of the best municipal health agencies in the world. But during the epidemic, the mayor has repeatedly ignored the advice of its top disease-control experts and sidelined the department.

“I think this is the culmination of months of conflict between the health department and City Hall,” said Councilman Mark Levine, who heads the Council’s health committee. “This reflects enormous frustration that global experts in infectious disease are being marginalized in the middle of a pandemic.”

Most recently, senior health department officials disagreed with Mr. de Blasio on what to do when staff or students in city schools test positive for the virus, according to a person with knowledge of the officials’ thinking.

Mr. de Blasio announced on Friday that a given school building could close, in some cases for 14 days, when two positive cases emerged and were not linked to the same classroom. The plan gives disease investigators some discretion on closure. But even with only 1 percent of tests coming back positive, as is the case in New York City now, health officials are still worried that the thresholds will lead to many schools closing at some point in the academic year, the person said.

Perhaps the most consequential debate inside City Hall over the coronavirus came during the second week in March. The city had a small number of positive cases, but its public health system was flashing a warning about the unchecked spread of a flulike virus.

Dr. Barbot and one of her top deputies began urging more restrictions on gatherings. Mr. de Blasio for a time sided instead with Dr. Katz, who had been advising City Hall against ordering shutdowns.

Some officials inside the health department talked about quitting that week, or staging a walkout to force action. Eventually, top officials and the mayor agreed on the need to lock down the city to stop the spread of the virus. Mr. de Blasio ordered schools closed on March 15.

Outside of the administration, some blamed Dr. Barbot for the delays and confusion, citing her shifting public statements on the virus from late January to early March. A few elected officials called for her to be fired in early April.

The turmoil at the top of the city’s health agency worsened in May over the mayor’s decision to locate the city’s contact-tracing efforts within its public hospital system and not in the health department.

Under Health + Hospitals, the city’s contact-tracing program got off to a rocky start. Lacking the capability to hire and manage 3,000 workers, it outsourced much of the day-to-day management of the call center at the core of its operations to Optum, a billion-dollar subsidiary of UnitedHealth Group.

Some workers said that the program in its first six weeks was frustrating, confusing and disorganized, and had ineffective protocols that led many people to hang up the phone before providing tracers with contacts. So far, fewer than half of New Yorkers who have tested positive for the coronavirus — some 20,000 people since the program began on June 1 — have shared their contacts.

“Right now, cases are popping up all over the place and we are not linking them to known contacts except in a small proportion of cases,” Dr. Neil Vora, the director of the trace effort, said at an internal town-hall-style meeting for tracers last month, a recording of which was provided to The Times.

Even with the new tracing program, the health department has been called on to handle more intricate aspects of so-called disease detective work, particularly in group settings like homeless shelters and nursing homes. That expanded to include restaurants and other social gatherings last month.

The mayor said on Friday that outbreaks in schools would also be handled by the health department, in coordination with the city’s new corps of contact tracers.

Joseph Goldstein and Sharon Otterman contributed reporting.