For employees of the Centers for Disease Control and Prevention, the hits keep coming.

The Covid-19 pandemic made the agency a frequent target of lawmakers and segments of the general public. Events took an even darker turn when a gunman opened fire on C.D.C. headquarters in Atlanta this month, spraying hundreds of bullets and killing a police officer.

And on Wednesday, employees reeled from news that the agency’s new director, Susan Monarez, had been fired after less than a month on the job — followed by her announcement that she was refusing to leave.

On Thursday morning, three senior officials were escorted from the building after announcing on Wednesday that they would quit over Health Secretary Robert F. Kennedy’s vaccine policies. Staff members gathered outside the C.D.C.’s gates to celebrate the leaders who had resigned.

“It’s brutal,” one employee said. “Everyone is in tears because we love and care about this agency so much.”

Mr. Kennedy has long held the agency in contempt, accusing its scientists of corruption and incompetence, and of hiding what he believes are links between some vaccines and autism.

He once compared immunizing children to practices in Nazi death camps.

“There’s a lot of trouble at C.D.C., and it’s going to require getting rid of some people over the long term in order for us to change the institutional culture,” Mr. Kennedy said at a news briefing on Thursday.