WASHINGTON — The top vaccine official with the Food and Drug Administration has resigned and criticized the nation’s top health official for allowing “misinformation and lies” to guide his thinking behind the safety of vaccinations.

Dr. Peter Marks sent a letter to Acting FDA Commissioner Sara Brenner on Friday saying that he would resign and retire by April 5 as director of the Center for Biologics Evaluation and Research.

In his letter, which was obtained by The Associated Press, Marks said he was “willing to work” to address the concerns expressed by Robert F. Kennedy Jr. about the safety of vaccinations. But he concluded that wasn’t possible.

“It has become clear that truth and transparency are not desired by the Secretary, but rather he wishes subservient confirmation of his misinformation and lies,” he wrote.

The U.S. Department of Health and Human Services did not respond to a request for comment.

Marks was offered the choice of resigning or being fired by Kennedy, according to a former FDA official familiar with the discussions, who spoke on condition of anonymity because he didn’t have permission to discuss the matter publicly.

Kennedy has a long history of spreading anti-vaccine misinformation, although during his Senate confirmation hearings he seemed to say he would not undermine vaccines. He promised the chair of the Senate health committee that he would not change existing vaccine recommendations.

Since becoming secretary, Kennedy has vowed to scrutinize the safety of childhood vaccinations, despite decades of evidence they are safe and have saved millions of lives.

Marks oversaw the agency’s rapid review and approval of COVID-19 vaccines and treatments during the pandemic.

Marks is credited with coining the name and concept for “Operation Warp Speed,” the effort under President Donald Trump to rapidly manufacture vaccines while they were still being tested for safety and efficacy. The initiative cut years off the normal development process.

Despite the project’s success, Trump repeatedly lashed out at the FDA for not approving the first COVID shots even sooner. Trump told confidants after his 2020 loss that he would have been reelected if the vaccine had been available before Election Day.

Dr. Paul Offit, a vaccine expert at Children’s Hospital of Philadelphia, criticized what he called the “firing” of Marks.

“RFK Jr.’s firing of Peter Marks because he wouldn’t bend a knee to his misinformation campaign now allows the fox to guard the hen house,” Offit said. “It’s a sad day for America’s children.”

Former FDA Commissioner Dr. Robert Califf said the issues raised in Marks’ resignation letter “should be frightening to anyone committed to the importance of evidence to guide policies and patient decisions.”

“I hope this will intensify the communication across academia, industry and government to bolster the importance of science and evidence,” he wrote.

The resignation follows news Friday that HHS plans to lay off 10,000 workers and shut down entire agencies, including ones that oversee billions of dollars in funds for addiction services and community health centers across the country.

In a post on social media Thursday, Kennedy criticized the department he oversees as an inefficient “sprawling bureaucracy.” He also faulted the department’s 82,000 workers for a decline in Americans’ health.

The resignation is the latest blow to the beleaguered health agency, which has been rocked for weeks by layoffs, retirements and a chaotic return-to-office process that left many staffers without permanent offices, desks or other supplies. Last month, Jim Jones, the FDA’s deputy commissioner for foods, resigned, citing “the indiscriminate firing” of nearly 90 staffers in his division, according to a copy of his resignation letter obtained by the AP.

Marks, who could not be reached for comment, also raised concerns in his letter about “efforts currently being advanced by some on the adverse health effects of vaccination are concerning” as well as the “unprecedented assault on scientific truth that has adversely impacted public health in our nation.”

He went on to detail the historic benefits of vaccinations dating back to George Washington and pointed to the ongoing measles outbreak as proof of what can happen when doubts about science take hold.

“The ongoing multistate measles outbreak that is particularly severe in Texas reminds us of what happens when confidence in well-established science underlying public health and well-being is undermined,” he wrote.

The measles outbreak, which could go on for months, has now spread to Kansas and Ohio after sickening more than 370 in Texas and New Mexico.

If it hits other unvaccinated communities across the U.S., as may now be the case in Kansas, the outbreak could endure for a year and threaten the nation’s status as having eliminated the local spread of the vaccine-preventable disease, public health experts said.

Casey reported from Boston. Perrone reported from Washington, D.C.