The deputy commissioner for public health at the New York State Health Department resigned in late summer. Soon after, the director of its bureau of communicable disease control also stepped down. So did the medical director for epidemiology. Last month, the state epidemiologist said she, too, would be leaving.

The drumbeat of high-level departures in the middle of the pandemic came as morale plunged in the Health Department and senior health officials expressed alarm to one another over being sidelined and treated disrespectfully, according to five people with direct experience inside the department.

Their concern had an almost singular focus: Gov. Andrew M. Cuomo.

Even as the pandemic continues to rage and New York struggles to vaccinate a large and anxious population, Mr. Cuomo has all but declared war on his own public health bureaucracy. The departures have underscored the extent to which pandemic policy has been set by the governor, who with his aides crafted a vaccination program beset by early delays.

The troubled rollout came after Mr. Cuomo declined to use the longstanding vaccination plans that the State Department of Health had developed in recent years in coordination with local health departments. Mr. Cuomo instead adopted an approach that relied on large hospital systems to coordinate vaccinations not only of their own staffs, but also of much of the population.

In recent weeks, the governor has repeatedly made it clear that he believed he had no choice but to seize more control over pandemic policy from state and local public health officials, who he said had no understanding of how to conduct a real-world, large-scale operation like vaccinations. After early problems, in which relatively few doses were being administered, the pace of vaccinations has picked up and New York is now roughly 20th in the nation in percentage of residents who have received at least one vaccine dose.

“When I say ‘experts’ in air quotes, it sounds like I’m saying I don’t really trust the experts,” Mr. Cuomo said at a news conference on Friday, referring to scientific expertise at all levels of government during the pandemic. “Because I don’t. Because I don’t.”

His comments reflected a rift between the state’s top elected official and its career health experts of the sort that has occurred across different levels of government during the pandemic. Former President Donald J. Trump warred publicly with Dr. Anthony S. Fauci, the nation’s top infectious disease expert, as well as officials at the Centers for Disease Control and Prevention.

Mayor Bill de Blasio forced out the head of New York City’s respected health department over the summer. Around the country, frustrated and overwhelmed public health officials have resigned in large numbers.

In Albany, tensions worsened in recent months as state health officials said they often found out about major changes in pandemic policy only after Mr. Cuomo announced them at news conferences — and then asked them to match their health guidance to the announcements.

That was what happened with the vaccine plan, when state health officials were blindsided by the news that the rollout would be coordinated locally by hospitals.

But it also occurred earlier with revisions in a host of state rules from the fate of indoor dining and businesses like gyms to capacity limits on social gatherings, according to a person with direct experience inside the department.

Earlier in the pandemic, the health officials were often informed about criteria for who was eligible to be tested for the virus — for example, an expansion to include essential workers like transit workers, police and firefighters — from Cuomo news conferences, the person said.

Dr. Howard Zucker, the state health commissioner, has remained in his post, and appears with Mr. Cuomo at news conferences.

But at least nine senior state health officials have left the department, resigned or retired in recent months. They include Elizabeth Dufort, the medical director in the division of epidemiology; Dr. Jill Taylor, the head of the renowned Wadsworth laboratory — which has been central to the state’s efforts to detect virus variants — and the executive in charge of health data, according to state records.

Additionally, the Health Department’s No. 2 official left for another job in state government, and another official, who helped oversee contact tracing, is expected to leave the department, also for another state government job.

Dr. Zucker said in a statement that the state was facing “an intense period of extraordinary stress and pressure and a different job than some signed onto.”

He added: “The Times’s point is several staff left — true, and many others joined the agency with the talents necessary to confront this new challenge.” The proof, he said, “is in the performance numbers.”

Mr. Cuomo’s handling of the pandemic has come under criticism in recent days after the state attorney general, Letitia James, said his administration had undercounted the tally of Covid-19 deaths of nursing home residents by not publicly disclosing deaths of those residents that occurred at hospitals.

Current and former health officials agreed to be interviewed about the crisis inside the public health bureaucracy only on condition of anonymity, saying that they feared retaliation for speaking out against the governor.

“Morale certainly was and continues to be at an all-time low,” one former health official said.

The former official pointed out that during past emergencies, the department rallied and morale soared as officials felt that their talent and experience were valued.

“In the pandemic, the opposite happened,” the former official said.

The departures came as the state prepared for and then stumbled through the early weeks of its vaccine campaign, in which experts said speed was paramount because of the threat posed by more contagious variants of the coronavirus.

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Vaccination policy was the latest one shaped largely by the governor’s office. Before that, officials said the State Health Department was not deeply involved in final decisions that have included allowing public events and mandating business closures based on color-coded “microclusters.”

Mr. Cuomo said in an interview that the scale of the pandemic had overwhelmed the state’s public health planning.

“It’s the Mike Tyson line: ‘Everybody has a plan until I punch them in the face,’” Mr. Cuomo said.

Mr. Cuomo said his approach had delivered results in New York, including a positivity rate that has been declining after a peak in early January and better vaccination rates. New York saw the worst of the pandemic in the spring, and roughly 43,000 have died, more than in any other state.

“The scale changes everything,” Mr. Cuomo said. “My job is to get the vaccinations done as soon as possible.”

In the fall, Mr. Cuomo shelved vaccine distribution plans that top state health officials had been drawing up, one person with knowledge of the decision said. The plans had relied in part on years of preparations at the local level — an outgrowth of bioterrorism fears following Sept. 11 — and on experience dispensing vaccine through county health departments during the H1N1 pandemic in 2009.

As a result, local officials across the state complained that their efforts to vaccinate were undercut by the Cuomo plan.

“Wait a minute, why are we not doing this?” Anthony J. Picente Jr., a Republican who is county executive in upstate Oneida County, said he remembered thinking.

At the New York City Health Department, officials had hoped to significantly expand a system used for childhood vaccinations, in which the city is able to order doses directly from the federal government, one city official said.

But the Cuomo administration, in an October letter to the Trump administration, told federal officials to work only with the state when it came to doling out doses. That made it difficult for the city to create its own vaccination sites, the official said.

State officials said the approach made sense for what was a statewide vaccination effort, and that the state’s plan incorporated guidance from the C.D.C. and lessons learned from previous health emergencies.

It is not possible to determine conclusively whether alternative plans at the state and local health departments would have performed better in the early weeks of the rollout. Public health departments have been chronically underfunded, a situation experts have warned of for years.

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  But elements of the state’s approach hindered the rollout, New York City officials contended.

  “Extensive red tape and unnecessary rigidity over who we could vaccinate and when — all with the looming threat of millions of dollars in punitive fines — made an extraordinarily difficult task all the more challenging in those first initial weeks of the rollout,” said Avery Cohen, a spokeswoman for Mayor de Blasio.

  In his own planning for the vaccine rollout, Mr. Cuomo spoke with hospital executives, outside consultants and a top hospital lobbyist in closed-door meetings. In December, Mr. Cuomo announced that the state would rely on large hospital systems as “hubs” to coordinate vaccinations, not simply for their own staff but also for ordinary New Yorkers.

  The state designated as a regional vaccination hub in New York City not the city’s 6,000-person Health Department, but rather the Greater New York Hospital Association, a trade group with a multimillion-dollar lobbying arm that had been a major donor to the governor’s causes.

  The approach included narrow eligibility rules and suffered from a lack of urgency by some hospitals. That led to fewer doses being administered in the early weeks, followed by abrupt shifts in policy that created a kind of free-for-all among those searching for vaccine appointments, according to interviews with more than two dozen current and former health officials, county leaders, vaccination experts and elected officials.

  “The governor’s approach in the beginning seemed to go against the grain in terms of what the philosophy was about how to do this,” said Dr. Isaac Weisfuse, a former deputy commissioner at New York City’s Health Department who often served as an incident commander during emergencies. “It did seem to negate 15 to 20 years of work.”

  Asked about the criticism, Mr. Cuomo said, “If Times reporters think I push hospitals too hard and local governments too hard, I say I’m a fighter for the people of New York and I believe I’m saving lives.”

  His aides said hospitals were made hubs because they had the necessary cold-storage capacity, particularly for the Pfizer-BioNTech vaccine; could operate regionally, not just in one county or city; and because health care workers were the first to be vaccinated.

  State officials said that Mr. Cuomo followed public health guidance in the vaccine rollout, including from the C.D.C., and that Dr. Zucker, the head of the department, has been closely involved in pandemic decisions.

  The governor speaks regularly with Dr. Michael Osterholm, an infectious disease expert at the University of Minnesota who serves on a Covid advisory panel put together by President Biden, and twice a week with Dr. Fauci, the officials said. (Dr. Osterholm and Dr. Fauci declined to comment.)

  The governor’s vaccine planning team has consisted mainly of longtime advisers, including Larry Schwartz, a former top aide and deputy county executive in two counties who is now an executive at an airport concession company.

  A task force with outside experts, convened by Mr. Cuomo to guide the vaccination plan, met infrequently and was rarely offered the chance to provide guidance.

  For help in planning the vaccination campaign, the governor turned to consultants from Deloitte and Boston Consulting Group. The in-house lobbyist for New York’s largest hospital system, Northwell Health, had direct involvement in the rollout.

  For about a month, starting in mid-October, the Northwell lobbyist, Dennis Whalen, worked from an office inside the State Health Department and helped shape the state’s approach. Mr. Whalen had worked previously as the department’s No. 2 official.

  “If you’re asked to help, you help,” Michael Dowling, the president of Northwell and a longtime ally of Mr. Cuomo, said. “There’s nothing nefarious about this at all.”

  It was a Northwell hospital nurse, Sandra Lindsay, who received the first Covid-19 vaccine dose in the nation in mid-December, an iconic moment in the pandemic, and a public relations victory for the private hospital system.

  The governor and his aides said the vaccine rollout was hamstrung by the federal government, which they blamed for a lack of vaccine. They also said that poor performance by the local authorities and public hospitals, particularly in New York City, slowed down distribution. Of late, Mr. Cuomo has regularly used his near-daily press briefings to call out hospitals by name that he said were not vaccinating quickly enough.

  After opening eligibility to many more people, New York now quickly uses its weekly shipments of vaccine, not including doses sent to the state through a federal program for nursing homes, state data shows.

  “We put together an operation where we used all the levers at our disposal to as quickly as possible vaccinate as many people as possible,” said Melissa DeRosa, the governor’s top aide, “and it obviously worked since we’re now oversubscribed and out of vaccine.”

  Still, Dr. Denis Nash, a professor of epidemiology at the City University of New York and a former senior city health official, said that giving such a large share of doses directly to hospitals meant that the government lost control of the pace of vaccinations during the program’s first month.

  “That was the bottleneck,” Dr. Nash said. “To put hospitals in charge of a public health initiative — for which they have no public health mandate, or the skills, experience or perspective to manage one — was a huge mistake, and I have no doubt that’s what introduced the delays.”

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