The abrupt departure of top leadership at the Centers for Disease Control in a dispute over policy directives from the Health and Human Services secretary, Robert F. Kennedy Jr., is causing a firestorm at both Atlanta and Washington.

After the agency’s director was fired Wednesday night, employees walked out of the Atlanta headquarters on Thursday and the Republican chairman of the Senate’s health committee warned against taking cues from the CDC’s vaccine advisory panel.

On Thursday afternoon, hundreds of people lined the streets outside of the CDC’s headquarters at Atlanta after the director, Susan Monarez, was dismissed by the president on Wednesday night. According to a livestream shared by the Associated Press, the crowd included CDC employees and anti-Kennedy activists. 

Several other CDC leaders responsible for combating infectious diseases left the building on Thursday after they made the decision to resign in protest over Mr. Kennedy’s policies, especially concerning vaccines. 

The Republican chairman of the Senate’s Health, Education, Labor, and Pensions Committee added to uncertainty about the direction of  vaccine policy on Thursday. If the vaccine advisory board goes ahead with a scheduled meeting next month, Senator Bill Cassidy said in a press release, any directives it sends out should be “rejected.”

Earlier this year, Mr. Kennedy fired and later replaced all 17 members of the Advisory Committee for Immunization Practices, which provides recommendations on which vaccines are safe for use. 

Dr. Cassidy, a physician himself, voiced concern at the time that the panel “will be filled up with people who know nothing about vaccines except suspicion.” Many of the new board members are noted vaccine skeptics.

Dr. Cassidy’s concerns appear only to have increased with this week’s developments at the agency.

“Serious allegations have been made about the meeting agenda, membership, and lack of scientific process being followed for the now announced September ACIP meeting,” Dr. Cassidy said Thursday in a prepared statement. 

“These decisions directly impact children’s health and the meeting should not occur until significant oversight has been conducted,” the Louisiana senator added.

“If the meeting proceeds, any recommendations made should be rejected as lacking legitimacy given the seriousness of the allegations and the current turmoil in CDC leadership.”

A spokesman for the Department of Health and Human Services did not immediately respond to an email seeking comment,

On Thursday, the White House said Ms. Monarez, a career scientist, was fired because she was not fulfilling the president’s goal of making America healthier.

The press secretary, Karoline Leavitt, did not elaborate on the reasons for the firing. However lawyers for Ms. Monarez told the Associated Press that she had refused “to rubber-stamp unscientific, reckless directives and fire dedicated health experts.”

Dr. Monarez, who had been in the post for only a month, initially resisted being fired by Mr. Kennedy, saying that only the president was allowed to fire her. Ms. Leavitt says the president officially relieved the director of her duties later on Wednesday.

“She was not aligned with the president’s mission to make America healthy again,” Ms. Leavitt told reporters. “The secretary asked her to resign. She said she would  resign and then she said she wouldn’t, so the president fired her.”

Dr. Cassidy cast the pivotal vote in getting Mr. Kennedy confirmed to his position as Health and Human Services secretary earlier this year. As chairman of the HELP committee, had Dr. Cassidy voted against the nomination, it would have failed and not been brought to the floor for a final vote. 

In a speech announcing his decision to back Mr. Kennedy for the job, Dr. Cassidy noted that the now-secretary had assured him that no changes would be made at the ACIP without consultations with members of Congress. 

“He has also committed that he would work within the current vaccine approval and safety monitoring systems, and not establish parallel systems. If confirmed, he will maintain the Centers for Disease Control and Prevention’s Advisory Committee on Immunization Practices without changes,” Dr. Cassidy said on the Senate floor in February. 

However, the senator is out of favor with the White House, being one of only seven Republican senators who voted to convict President Trump at his impeachment trial in 2021. He faces a potentially tough primary challenge ahead of next year’s midterm elections.