As Mayor Bill de Blasio was resisting calls in March to cancel large gatherings and slow the spread of the coronavirus in New York City, he found behind-the-scenes support from a trusted voice: the head of his public hospital system, Dr. Mitchell Katz.

There was “no proof that closures will help stop the spread,” Dr. Katz wrote in an email to the mayor’s closest aides. He believed that banning large events would hurt the economy and sow fear. “If it is not safe to go to a conference, why is it safe to go to the hospital or ride in the subway?” he wrote. And, he said, many New Yorkers were going to get infected anyway.

“We have to accept that unless a vaccine is rapidly developed, large numbers of people will get infected,” he wrote. “The good thing is greater than 99 percent will recover without harm. Once people recover they will have immunity. The immunity will protect the herd.”

For Mr. de Blasio, the arguments in Dr. Katz’s March 10 email, obtained by The New York Times, appeared to hold sway over the calls for greater restrictions on daily life from top Health Department officials, who were alarmed by public health surveillance data pointing toward a looming outbreak.

Now, as the crisis in New York City enters the next stage, Mr. de Blasio, Dr. Katz and Health Department officials are once again navigating a nasty public fissure.

Health experts fear that their rift may threaten the city’s ability to limit the spread of the disease once the city — which has seen more than 20,000 people die of the virus — begins to reopen.

The mayor last week shocked the Health Department by taking away its authority to oversee contact tracing, giving the job to Health and Hospitals, the agency overseen by Dr. Katz. It is a monumental task: The city must build and run an army of some 2,500 people to track and trace the close contacts of every infected person.

The mayor’s decision to shift the responsibility to the public hospital system illustrated how Mr. de Blasio’s faith in Dr. Katz’s leadership abilities took precedence over the experience and knowledge of his public health officials, who have clashed with the mayor over a variety of issues.

Epidemiologists, former public health officials and the city comptroller criticized the move, pointing out that the Health Department has for decades expertly performed contact tracing for diseases like tuberculosis and H.I.V., and had been preparing for two weeks to run the expanded tracing operation for Covid-19, the disease caused by the coronavirus.

On Tuesday, the city comptroller, Scott M. Stringer, requested documents from City Hall as part of a formal investigation into the city’s response to the pandemic, including its handling of public health recommendations. On Friday, the City Council will hold a hearing on the mayor’s decision to give Health and Hospitals control of the contact tracing effort.

Even the person who ran the city’s hospital system before Dr. Katz thought the move was a mistake.

“It is a head-scratcher. I can’t figure out the rationale, and I don’t think it’s worth the risks,” said Stanley Brezenoff, who was chosen by Mr. de Blasio in 2016 to temporarily lead Health and Hospitals. “Just because they both have ‘health’ in the name doesn’t mean they’re in the same business.”

“I’m second to none in my admiration for Mitch’s clinical prowess,” Mr. Brezenoff added, “but this is a job for the Health Department.”

Dr. Katz, who is well regarded in the hospitals field, declined to comment for this article. His defenders said it was important to view his March 10 email about keeping the city open within the context of that time. Public health experts were wrestling with a highly unusual series of factors, and there was a wide range of opinions about how to respond.

The mayor’s press secretary, Freddi Goldstein, when asked about the March 10 email, said that the mayor had sought advice from many experts, and that a range of individuals including Dr. Katz and the health commissioner, Dr. Oxiris Barbot, “gave the best advice based on what they knew at that time.”

Ms. Goldstein said the decision to place its new contact tracing corps under the control of Health and Hospitals was rooted in the need for a “single, streamlined entity” to manage the program, along with the city’s diagnostic testing efforts and oversight of care for infected patients isolated in hotels.

“While the academic and expert knowledge that the Health Department brings are essential pieces,” Ms. Goldstein said in an email, “the ability to rely on the organizational infrastructure that H+H brings is also essential.”

The mayor, she said, wanted the city to “capitalize on both.”

Mr. de Blasio, Dr. Katz and senior city officials have insisted that Health and Hospitals — a quasi-private organization controlled by the government — was chosen largely for practical reasons. Because of its structure, it could hire people and award contracts more quickly than the Health Department, a city agency that generally must follow city procurement policies.

But during the coronavirus crisis, the hiring and contracts had already been taken over by a foundation, the Fund for Public Health in New York, which works with the Health Department; the city has also streamlined Covid-19-related spending by suspending typical procurement requirements.

Ms. Goldstein contended that Health and Hospitals had built-in advantages, including access to supply chains, clinical surge staffing contracts, telemedicine and reference lab contracts. It made sense to give the tracing program to the hospitals, she added, so that the major components of the city’s future efforts to control the virus — testing, tracing, isolation — could be run under one roof.

An effective contact tracing program must be up and running before New Yorkers can begin to safely emerge from their lockdown, public health officials said. Getting such a system ready is a daunting challenge — even without any stumbles or political infighting.

But since taking office in 2014, Mr. de Blasio has found himself routinely at odds with his own public health officials, differing on issues including a proposed ban on horse carriages in Central Park and an outbreak of Legionnaires’ disease in the Bronx.

Current and former administration officials said the conflict stemmed from Mr. de Blasio’s apparent distrust of experts and his dissatisfaction with public health recommendations, which are often based on scientific analysis of imperfect and at times incomplete information.

The mayor prizes certainty, decisiveness and directness, aides and former officials said. Dr. Katz, a well-regarded leader who came to New York after holding top public health positions in San Francisco and Los Angeles, often presented Mr. de Blasio with information in the way the mayor favored.

“He understands the importance of making clear, definitive decisions for the top elected official he’s working for,” Eric Phillips, the mayor’s former press secretary who now works in crisis management for the public relations firm Edelman, said of Dr. Katz. “That’s why the mayor trusts his judgment. Dr. Katz is not afraid to take a complicated subject, give his opinion and make a recommendation.”

That dynamic emerged again in the early days of the coronavirus outbreak. By the second week of March, the city’s public health warning system — known as the syndromic surveillance system — began strongly signaling the spread of a flulike illness, officials said.

City Hall wanted to see firm numbers of positive test results before ordering closures. Publicly, as well as in guidance to other agencies as late as March 9, the Health Department was not recommending the closure of events, like the city’s half marathon, according to an email shared with The Times.

But inside the department, staff members were deeply concerned that their warnings were not getting through. Some were ready to walk out in protest; others were threatening to quit.

In his March 10 email to top city officials, Dr. Katz made the case that keeping the city open was the best approach at the time.

“Canceling large gatherings gives people the wrong impression of this illness,” he wrote. “Many of the events are being canceled anyway, and fewer people are going out. However, it is very different when the government starts telling people to do this.”

He wrote that Italy “is having a terrible problem that I do not believe we will have,” and ended the message by arguing that shutting down events could create fear among some with mental health issues.

“If even a few people with serious mental illness become more isolated or fearful due to messaging, we could have more permanent harm than we currently have with Covid-19,” he wrote in the email, which was sent to three deputy mayors, top health officials and the budget director.

Ms. Goldstein said Dr. Katz stood by his concern over the harm caused by isolation to those with mental illness and by his comments on herd immunity.

She added that if there was anything to be second-guessed, it would be the shifting guidance from the Centers for Disease Control. “The C.D.C. repeatedly misled us and greatly hampered our ability to catch and respond to this disease,” she said.

Part of Dr. Katz’s reasoning in March for opposing closures, particularly of city schools, was that it would lead to health care workers not showing up to work — a concern shared by leaders of New York’s private hospitals. Kenneth E. Raske, the president of the Greater New York Hospital Association, said large gatherings were a “corollary issue” to the question of closing schools.

Michael Dowling, the chief executive of Northwell Health, the state’s largest health care provider, said, “Mitch was asking questions that a lot of people were asking at that point.”

But Mr. Dowling also recalled that on March 10, the day that Dr. Katz sent the email, Northwell decided to cancel all of its in-person executive meetings, after a top hospital leader involved in the pandemic response tested positive for Covid-19.

That same day, Dr. Katz appeared with the mayor at a news conference at Bellevue Hospital, one of 11 public hospitals in the city’s system. In spite of signs that the virus’s presence was growing, Dr. Katz gave an optimistic report, saying the system was ready to handle a surge in patients.

His confidence — and his arguments in favor of keeping the city open — increased his stature with the mayor, said two people with knowledge of City Hall discussions.

His influence grew further during that period in March, as the mayor sought an expansion of testing and the city began opening testing sites at public hospitals. The Health Department objected at the time, saying that outpatient testing sites would draw those with the disease into contact with those who were not yet infected.

Mr. de Blasio’s decision to take the contact tracing program away from Health Department leadership may have been the most public example of their fractured relationship, but their conflicts stretch back to the mayor’s first term.

Aides to the mayor, looking to help him deliver a campaign promise to ban horse-drawn carriages from Central Park, sought assistance from the Health Department, said Daniel Kass, a former deputy health commissioner.

“City Hall tried to enlist the Health Department to support the argument that the stables were unfit, and that horses were injured at a high rate on the streets in New York,” Mr. Kass said. “The Health Department had no data to support those arguments.”

The rift widened during the Legionnaires’ disease outbreak in 2015 in the Bronx that killed 12 people. The Health Department had identified five buildings in the Bronx as the source of the disease, but Mr. de Blasio wanted the department to test cooling towers broadly across the city.

That struck officials as illogical, but Mr. de Blasio was insistent. In one gathering of roughly 50 people at Lincoln Hospital in the Bronx, the mayor appeared eager for other city agencies to step in, and he looked to his buildings commissioner for possible assistance.

“Do you need helicopters?” Mr. de Blasio asked, according to a person who was present at the meeting. The dumbfounded buildings commissioner said he did not. Mr. de Blasio upbraided him, and then stormed out of the meeting.

“The mayor was elected to protect and advocate for New Yorkers — that’s what he did,” Ms. Goldstein said of the Legionnaires’ episode.

Another flare-up emerged during the coronavirus outbreak, when the mayor interceded in an argument in late March between Dr. Barbot and Terence Monahan, the highest-ranking uniformed member of the Police Department. Chief Monahan had demanded that the Health Department relinquish hundreds of thousands of protective masks for the police force to use.

The mayor sided with Chief Monahan; the roughly seven-week-old confrontation, reported by The New York Post late Wednesday, led Dr. Barbot to apologize, according to her spokesman.

An official at the Health Department said Dr. Barbot’s remarks came after Police Department officials had shown up at a secure Health Department warehouse and tried to commandeer 500,000 N-95 masks that were earmarked for hospitals. Chief Monahan said in an interview that the city’s Office of Emergency Management had given the go-ahead to pick up 250,000 masks; when police showed up to the warehouse, they were told they were to receive only 50,000 masks.

During the confrontation, Dr. Barbot told Chief Monahan that she did not “give two rats’ asses about your cops,” according to The Post. The alleged remark drew vitriolic criticism from police unions, including the Sergeants Benevolent Association, which referred to Dr. Barbot as a “bitch” who had “blood on her hands” in a tweet.

After the mayor’s office intervened, the police were given 250,000 masks.

Mr. de Blasio said on Thursday that he was not previously aware of the heated argument, and that he planned to discuss it with Dr. Barbot. “If what was reported was accurate, the commissioner needs to apologize to the men and women of the N.Y.P.D.,” he said.

The episode was emblematic of the growing rift between City Hall and the Heath Department, a state of affairs that Denis Nash, a professor at the C.U.N.Y. School of Public Health who served as director of H.I.V./AIDS surveillance at the Health Department, said was “incredibly tragic.”

“It seems to be getting worse when we’re in the middle of a public health crisis,” he said. “I worry that a rift like that could cost many lives in New York.”

Ashley Southall contributed reporting.

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