Among those leaving the agency was Dr. Demetre Daskalakis, director of the CDC's National Center for Immunization and Respiratory Diseases.
"I am not sure who the Secretary is listening to, but it is quite certainly not to us," he wrote.
Daniel Jernigan, director of the CDC's National Center for Emerging and Zoonotic Infectious Diseases, has also resigned.
"Over the last few months, it really has been a different approach to things," he said. "We were asked to host a number of individuals that were brought in specifically to review and revise scientific information we had thought was settled—information about vaccines and vaccine safety."
Jernigan also said, "I have come to that point where I'm not able to fulfill the duties that I have as a public health professional in this environment."
Also exiting is Debra Houry, the CDC's chief medical officer, who said that Monarez's attempts to be transparent, including posting documents for public comment, had been blocked.
"She was given feedback from HHS that those couldn't happen, and she was called to a meeting with the secretary on Monday," Houry said. "For us, we knew that if our scientific leader couldn't make changes like that, we could no longer stay."
HHS did not respond to a request for comment.
Several other CDC employees, among them Dr. Peter Marks, the Food and Drug Administration's top vaccine official during the COVID-19 pandemic, had previously stepped down over disagreements with Kennedy.
Kennedy said during an appearance on Fox News on Aug. 28 that there are problems with the CDC, including its promotion of social distancing, masks, and school closures during the COVID-19 pandemic, as well as its current support of fluoridation.
He also said, "We need strong leadership that will go in there and that will be able to execute on President Trump’s broad ambitions."
White House press secretary Karoline Leavitt, in a briefing in Washington on Aug. 28, drew attention to Daskalakis's reference to "pregnant people" as opposed to pregnant women.
"That's not someone we want in this administration anyway," she said.
"If people are not aligned with the president's vision, and the secretary's vision, to Make America Healthy Again, we will gladly show them the door," Leavitt added.
A replacement for Monarez will be named soon by Trump or Kennedy, according to the White House.
Some lawmakers have raised concerns about the ouster of Monarez and the CDC resignations.
Monarez's lawyers said she declined to sign off on what they described as "unscientific, reckless directives" and fire certain employees, causing her to be targeted. Mark Zaid, one of the lawyers, declined to provide further details.
The lawyers also maintain that because Monarez was notified of her firing by a White House staffer, rather than the president, she is still the CDC's director.
"The president fired her," Leavitt said, "which he had every right to do."