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But now, with a single temporary Monday from a federal judge in Boston, the momentum Kennedy had reached through those actions has been abruptly halted.

The development disrupts Kennedy’s push to remake vaccine policy at a key political moment, when the White House and the U.S. Department of Health and Human Services had appeared to be moving beyond vaccine efforts and toward a less contentious agenda on healthy food ahead of November’s midterm elections.

It remains to be seen whether the ruling will energize Kennedy’s supporters to fight back, provide cover for the administration to more firmly leave vaccines in the past, or both.

HHS spokesman Andrew Nixon said in a statement that the department “looks forward to this judge’s decision being overturned.” Deputy Attorney General Todd Blanche said the administration would appeal and noted that another of the judge’s rulings, on immigrant deportations, was lifted by a federal appeals court on Monday.

“How many times can Judge Murphy get reversed in one year?” Blanche wrote on X. “We will keep appealing these lawless decisions, and we will keep winning. The question is, how much embarrassment can this Judge take?”

Judge’s ruling sharply rebukes Kennedy’s approach

After Kennedy dropped his own independent presidential bid and threw his support behind Trump two years ago, Trump vowed to reward Kennedy by letting him “go wild” on health, food and medicine.

The health secretary has done just that, including moving at a blistering pace last year to overhaul public health guidance and revamp long-held precedents in vaccine policymaking.

Judge Brian Murphy said in Monday’s order that Kennedy disregarded certain long-held government processes, including reconstituting a scientific committee that advises the Centers for Disease Control and Prevention on vaccines, in a way that likely violated federal law.

“There is a method to how these decisions historically have been made – a method scientific in nature and codified into law through procedural requirements,” Murphy wrote. “Unfortunately, the Government has disregarded those methods and thereby undermined the integrity of its actions.”

Mark Gorton, president of the Kennedy-aligned MAHA Institute, said the judge was misguided in viewing the HHS bureaucratic process before Kennedy as “some sort of ideal.”

“You’ve had all sorts of ACIP decisions for decades, and you never had a judge standing up and saying that his judgment is superior to that of the panelists, even though the ACIP members for years have been incredibly corrupt and incredibly conflicted,” Gorton said.

Kennedy’s allies say a ‘rogue’ judge could reinvigorate their movement

Dr. Robert Malone, one of Kennedy’s appointees on the vaccine advisory committee, accused Murphy of being a “rogue” judge and called for his impeachment.

He urged the Trump administration to keep pursuing Kennedy’s vaccine policy changes, writing on Substack that the temporary ruling “is a delay, not a defeat.”

For at least one Kennedy ally, the ruling is an opportunity. Jeffrey Tucker, founder of the nonprofit Brownstone Institute who has rallied support behind Kennedy, said he sees it as a “clarifying moment” that will bring MAHA activists together after some and infighting.

“It makes the battle lines really, really obvious to everybody,” Tucker said. “It’s an opportunity for moral courage, strategic intelligence and doubling down in dedication to the agenda of medical freedom above all else.”

The ruling could give the administration cover to leave unpopular policies in the past

But the decision also comes at a time when Republican pollsters have warned that Kennedy’s vaccine stances could be a liability in the midterms – and when the White House and HHS had been moving on to less contentious pursuits.

Earlier this week, a White House official who requested anonymity to freely discuss the administration’s thinking said Kennedy had already achieved much of what he had set out to do on vaccines, and the administration was doubling down on food this year.

A White House spokesperson didn’t immediately respond to an inquiry Tuesday about how the ruling will affect that approach.

Sara Rosenbaum, a professor of health law and policy at George Washington University, said the judge’s ruling happened as the administration already understood that “Kennedy had gotten them into a very bad place.”

“I think it hopefully will toughen their resolve to keep getting vaccines off the agenda for now,” she said.