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…

[A]t 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.