WASHINGTON —

President Trump has decided to indefinitely delay the nomination of a new director for the Centers for Disease Control and Prevention, according to three senior administration officials, as the White House struggles to reconcile the radical public health overhaul sought by Health Secretary Robert F. Kennedy Jr. with the political necessity of maintaining public confidence in routine childhood immunizations.

The delay leaves the nation’s premier public health agency under the stewardship of an acting director at a time when Mr. Kennedy, confirmed as Secretary of Health and Human Services earlier this year, is pushing for a fundamental restructuring of how the government handles food safety, chronic illness, and environmental toxins.

The ‘Kennedy Factor’

Since taking the helm of HHS, Mr. Kennedy has championed a “Make America Healthy Again” (MAHA) agenda, focusing on the “toxic” food supply and the rising rates of chronic disease in children. However, his long history of questioning vaccine safety has created a significant hurdle in the search for a C.D.C. leader.

According to sources familiar with the selection process, several candidates who align with Mr. Kennedy’s views on ultra-processed foods and chemical regulation were ultimately deemed “unconfirmable” by White House transition advisers due to their public statements on vaccines. Conversely, more traditional public health figures, who might easily clear a Senate confirmation hearing, have been rejected by Mr. Kennedy’s team for being too closely aligned with the “medical-industrial complex” he has vowed to dismantle.

“We are looking for a Goldilocks candidate,” said one White House official who spoke on the condition of anonymity to discuss internal deliberations. “Someone who understands the need for systemic change in how we address chronic disease, but who doesn’t trigger a mass resignation at the agency or a firestorm in the Senate over vaccine policy.”

Shortlist in Flux

Names that have circulated in recent weeks include Dr. Jay Bhattacharya, a Stanford professor known for his opposition to Covid-19 lockdowns, and Dr. Joseph Ladapo, the Florida Surgeon General. While both are favorites of the MAHA movement, internal polling suggests that Dr. Ladapo’s previous guidance against certain vaccines could make his confirmation a bruising battle the administration is not yet ready to fight.

Other potential picks, such as Dr. Casey Means, a prominent voice in the metabolic health movement, have been praised by Mr. Kennedy but lack the administrative experience typically required to run an agency with 11,000 employees and a $17 billion budget.

The Risks of a Vacancy

The prolonged vacancy has sparked concern among public health experts and career scientists within the C.D.C., who warn that the lack of a permanent director hampers the agency’s ability to respond to emerging threats, such as the ongoing H5N1 avian flu monitoring.

“The C.D.C. is an agency that runs on institutional trust,” said Dr. Thomas R. Frieden, a former director of the agency. “Every day that goes by without a confirmed leader who is viewed as scientifically rigorous and politically independent, that trust erodes further. You cannot run public health by committee or by acting director indefinitely.”

Republican leaders in the Senate have reportedly signaled to the White House that they would prefer a nominee with a traditional medical background to avoid a public debate over vaccine efficacy—a debate many GOP lawmakers fear could alienate moderate voters and suburban parents.

A Pivot to Policy First?

For now, the administration appears content to let Mr. Kennedy drive policy from the secretarial level while the C.D.C. remains in a holding pattern. Sources suggest the President may wait until after the upcoming mid-term primary season to name a nominee, hoping to avoid making the C.D.C. a central theme of the campaign trail.

In the interim, Mr. Kennedy has begun installing his own advisers in deputy roles at the agency, moving to implement changes to fluoride recommendations and food coloring regulations—areas where there is more political consensus than the contentious issue of vaccines.

But as the search continues, the central question remains: Can the Trump administration truly “disrupt” public health without alienating the very scientists and citizens required to make those changes a reality?