Sidelined by Cuomo, nine top New York State health officials have quit in recent months.

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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 high-level departures 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 designed a vaccination program hampered 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.

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.

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.

At least nine senior state health officials have left the department, resigned or retired in recent months. They include Dr. Elizabeth Dufort, the medical director in the division of epidemiology; and 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.

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