Health Secretary Robert F. Kennedy Jr. summoned Susan Monarez, the director of the Centers for Disease Control and Prevention, to his office in Washington earlier this week to deliver an ultimatum.

She needed to fire career agency officials and commit to backing his advisers if they recommended restricting access to proven vaccines — or risk being fired herself, according to people familiar with the events.

Dr. Monarez’s refusal to do so led to an extraordinary standoff on Thursday that paralyzed the nation’s health agency, which is still reeling from mass layoffs and a shooting this month that killed a police officer and terrified employees.

Top officials have quit, Dr. Monarez’s future is in doubt and President Trump has yet to publicly back his health secretary. But late Thursday night, Mr. Kennedy sent an email to C.D.C. employees saying he had installed his deputy, Jim O’Neill, a former biotechnology executive, as the agency’s acting director.