The new director of the Centers for Disease Control and Prevention, Susan Monarez, has been fired by the White House after she refused orders to resign. Ms. Monarez, who was just weeks into the job, had been clashing with the Department of Health and Human Services secretary, Robert F. Kennedy Jr.

“Since Susan Monarez refused to resign, despite informing HHS leadership of her intent to do so, the White House has terminated Monarez from her position with the CDC,” a White House spokesman, Kush Desai, said in a statement on Wednesday evening.

Ms. Monarez’s attorneys, Mark S. Zaid and Abbe Lowell, claimed in a statement that their client had “neither resigned nor received notification from the White House that she had been fired, and as a person of integrity and devoted to science, she will not resign.”

The attorneys accused Mr. Kennedy of “weaponizing public health for political gain” through radical vaccine policy reforms and mass firings of public health officials. 

“When CDC Director Susan Monarez refused to rubber-stamp unscientific, reckless directives and fire dedicated health experts, she chose protecting the public over serving a political agenda. For that, she has been targeted,” her attorneys said in their statement.

Mr. Desai, at the White House, fired back. “As her attorney’s statement makes abundantly clear, Susan Monarez is not aligned with the President’s agenda of Making America Healthy Again,” he said.

In a statement on X, HHS confirmed that Ms. Monarez was “no longer director of the Centers for Disease Control and Prevention.”

“We thank her for her dedicated service to the American people,” HHS said.

Ms. Monarez’s brief tenure as CDC director — she was sworn in by Mr. Kennedy on July 31 — was complicated by the health secretary’s insistence on overhauling the nation’s vaccine policy.

Ms. Monarez, who is a scientist and the first CDC chief without a medical degree in more than 70 years, “was pressed for days by Kennedy, administration lawyers and other officials over whether she would support rescinding certain approvals for coronavirus vaccines,” the Washington Post reported Wednesday.

On Monday, Ms. Monarez was reportedly asked by Mr. Kennedy and other officials if she was “aligned with the administration’s efforts to change vaccine policy,” and was pressured to fire members of her senior staff by week’s end, according to the Washington Post.

When she balked, Mr. Kennedy then urged her to resign for “not supporting President Trump’s agenda.” Ms. Monarez, in turn, refused to resign and instead contacted Senator Bill Cassidy, a Republican of Louisiana who is a physician and a key senator on matters of health policy. 

Dr. Cassidy, who voted in favor of Mr. Kennedy during his Senate confirmation as health secretary, has openly questioned the HHS’s recent decisions to curb nearly $500 million in mRNA vaccine research and to fire the entire Advisory Committee on Immunization Practices panel, replacing many of them with noted vaccine skeptics.

Dr. Cassidy “privately pushed back on Kennedy’s demands,” which enraged the health secretary and caused him to admonish Ms. Monarez further, according to the Washington Post. She was then told by Trump administration officials to either resign or be fired.

Before joining the CDC, Ms. Monarez was the deputy director of the Advanced Research Projects Agency for Health and worked in the White House’s Office of Science and Technology Policy and on the National Security Council, according to her online bio. 

In January, she was named acting CDC director at about the same time President Trump named a longtime vaccine skeptic and former congressman, Dave Weldon, a Republican of Florida, as his first pick for the role. 

However, in March, Mr. Trump withdrew his nomination for Mr. Weldon less than an hour before his Senate confirmation hearing after the former congressman acknowledged “there were not  enough votes to get me confirmed.”

Mr. Trump nominated Ms. Monarez as director, forcing her to step down as acting director in March and leaving the agency leaderless in the interim. In her absence, Mr. Kennedy assumed direct control of the agency and set about reforming the CDC’s vaccine policy. In May, he announced on X that the CDC would remove the Covid-19 vaccine from the agency’s recommended immunization schedule for healthy children and healthy pregnant women. In June, Mr. Kennedy fired all 17 ACIP board members, replacing them with his handpicked board of new advisors, many of them with noted histories of vaccine skepticism. Ms. Monarez was confirmed on July 31.

The development of the mRNA vaccine to combat Covid was a signature achievement of Mr. Trump’s first term. In August, Mr. Kennedy enforced a “coordinated wind-down” of its mRNA vaccine development programs, valued at nearly $500 million. 

“As the pandemic showed us, mRNA vaccines don’t perform well against viruses that infect the upper respiratory tract,” Mr. Kennedy said in a YouTube video. 

On August 8, a gunman who was “discontent” over the Covid-19 vaccine fired more than 500 rounds at the CDC headquarters at Atlanta, killing a police officer and later himself. 

Also on Wednesday, Mr. Kennedy announced on X that he had rescinded the emergency use authorizations for Covid-19 vaccines “once used to justify broad mandates on the general public during the Biden Administration.”

In addition, the Food and Drug Administration approved updated Covid-19 vaccines for adults 65 and older. By removing the emergency use authorizations, patients will now have to consult with their doctor to receive a shot instead of doing so directly at a pharmacy.

“These vaccines are available for all patients who choose them after consulting with their doctors,” Mr. Kennedy said on X.

In addition to Ms. Monarez, the CDC’s chief medical officer and the director of its infectious-disease center were ousted on Wednesday, along with other officials, according to the Washington Post.