After six months of turmoil, the loss of the new director and a round of high-profile resignations marks a new low, some employees said.

© Nicole Craine for The New York Times

The director, Susan Monarez, declined to fire agency leaders or to accept all recommendations from a vaccine advisory panel made over by Mr. Kennedy, according to people with knowledge of the events.

© Nicole Craine for The New York Times

Susan Monarez was said to have refused to adopt Health Secretary Robert F. Kennedy Jr.’s stance on vaccination policy. A lawyer for Dr. Monarez said the firing was “legally deficient.”

© Tierney L. Cross/The New York Times