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Health & Science

CDC Acting Director Tells Staff He’s Had ‘Scientific’ Disagreements With RFK Jr.

In an internal meeting, Jay Bhattacharya spoke candidly about his relationship with Kennedy, expressed support for the measles vaccine and said his replacement is coming soon.

Jay Bhattacharya

Jay Bhattacharya is the acting director of Centers for Disease Control and Prevention and the director of the National Institute of Health. Jacquelyn Martin/AP

By Margaret Manto

March 25, 2026 03:04 p.m.

Updated: March 25, 2026 03:04 p.m.

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Centers for Disease Control and Prevention acting Director Jay Bhattacharya told agency staff Wednesday he has had “scientific” disagreements with Health Secretary Robert F. Kennedy Jr.

“Do we agree on every single item? No,” Bhattacharya said of Kennedy during an internal Q&A session, according to audio obtained by NOTUS. He added, “We may have disagreements about scientific matters, but he listens.”

More specifically, Bhattacharya, a Stanford University professor and health economist who rose to prominence as a critic of COVID-19 shutdown policies, said he would continue to strongly encourage parents to vaccinate their children.

“The way that we actually get back to having basically zero measles transmission is by making sure that every community in the country knows that this is the best way to protect their kids from this deadly disease,” Bhattacharya told staff.

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“Bobby’s fine with me saying that,” he added.

Vaccines were one of many topics Bhattacharya spoke about during the Wednesday morning session at the CDC headquarters in Atlanta, his first appearance before the agency’s entire workforce since being named acting director in February, when the former acting director, Jim O’Neill, was dismissed.

Since then, Bhattacharya has served concurrently as head of both the CDC and the National Institutes of Health.

Kennedy has a history of casting doubt on vaccines and has drawn scrutiny for not highlighting them as the best way to control the ongoing measles outbreak. His hand-selected panel of vaccine advisers has voted to remove the hepatitis B birth-dose vaccine from the childhood immunization schedule and to split up vaccines long given in tandem. (A federal judge blocked some of those efforts last week, saying Kennedy’s decision to replace the panel did not follow federal legal procedures.)

In contrast, since becoming acting CDC director, Bhattacharya has received praise from agency staff for speaking publicly about the benefits of vaccines.

After publication, Bhattacharya responded to NOTUS’ reporting on X.

“I differ on scientific matters with nearly everyone about some things,” he wrote. “I learn much from respectful conversations about those disagreements, including especially with Sec. Kennedy.”

Bhattacharya’s time at the agency may soon come to an end: He told staff on Wednesday that he expects his permanent replacement to lead the public health agency to be announced imminently.

“I anticipate that there will be a permanent director nominated by tomorrow,” Bhattacharya said.

That news came with a word of caution Wednesday: Senate confirmations are “a long, painful – I know from experience — process.” He told staff he would stay on as CDC acting director until a new permanent director is sworn in.

Acting directors can only serve for a maximum of 210 days from the date a vacancy occurs. It has been 210 days today since the last permanent director, Susan Monarez, was fired in August.

The short list of potential candidates for the role include former Kentucky Governor Ernie Fletcher, who is also a family physician, and Joseph Marine, a cardiologist at Johns Hopkins, Bloomberg reported.

The CDC has been in a state of chaos since Kennedy took over the health department, including mass layoffs last October, a partial reversal of those layoffs, Monarez’s dismissal over scientific disagreements and a shooting on campus that left employees rattled.

Employees pressed Bhattacharya on his commitments to the agency. The acting director said he was bringing their concerns to HHS leadership, including “emphasizing in no uncertain terms” to HHS that telework accommodations for CDC employees should be “treated with the respect they deserve.”

Bhattacharya also said he had not heard of any future reductions in force, but that he would oppose them.

CDC employees also pressed Bhattacharya on the agency’s ongoing efforts to recuperate after the shooting at CDC headquarters in August, during which a gunman killed one police officer, David Rose, and fired hundreds of rounds at CDC buildings.

Bhattacharya said that repairs to broken windows that are still boarded up were planned, but he didn’t have an exact timeline. He also said he had suggested to Kennedy that the road leading into CDC’s campus be renamed after Rose, and that Kennedy was on board with the plan, which drew applause from the audience, according to the audio.

On other issues, like the U.S.’s withdrawal from the World Health Organization, Bhattacharya remained mum.

“The politics of the WHO withdrawal are above my pay degree,” he said.

While some of the acting director’s comments were well-received — especially those relating to supporting hiring at the agency, including rehiring some employees who worked on chronic disease and were affected by last year’s reductions in force — the mood in the room was still on edge, one CDC employee who attended the meeting in person told NOTUS.

“There was tension,” the employee said. “We were trying to be respectful while still feeling very wary.”

The employee said that a number of non-CDC security personnel were present at the meeting, which they called “a first for any all-staff or all-hands I have seen.”

“Do they really think that little of us? Like we are going to bum rush the stage and attack?” the employee said.

Several other attendees who asked questions in person thanked Bhattacharya for his transparency.

“Thank you for your candor and this opportunity to ask you real questions, even the tough ones,” one participant said.

“It has been several years since we’ve had an open mic, so thank you for doing that, and we hope this will continue when a new director is appointed as well,” said another.

Author

fellow2024_margaretmanto_500px.png Margaret Manto is a former NOTUS reporter and Allbritton Journalism Institute fellow.

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