In a hearing this month, Isaac Belfer, a lawyer for the Trump administration, argued that Mr. Kennedy and the committee had “unreviewable” — or absolute — authority to make vaccine policies, even if that included recommending that people become infected with measles instead of getting vaccinated.
Judge Murphy was clear in his dismissal of that argument. “Suffice it to say that the Court disagrees,” he said.
The decision was the clearest outcome yet in an escalating battle between the medical establishment and the Health Department, which under Mr. Kennedy has embraced anti-vaccine conspiracies, including debunked theories that childhood shots cause autism, asthma or other diseases.
“This is a significant victory for public health, evidence-based medicine, the rule of law, and the American people,” Richard Hughes, a lawyer for the plaintiffs, told reporters after the court made its ruling.
The government may appeal the decision, Mr. Hughes noted, “but for now, we get to celebrate a rare bit of good news.”
The vaccine committee’s decisions powerfully influence states’ vaccination requirements for entry into day care and elementary school and shape insurance coverage of the shots.
The panel was initially scheduled to meet in February, but the Health Department did not file the necessary federal notices for the meeting and postponed the session.
The lawsuit was filed in July by the medical organizations, including the American Academy of Pediatrics, after Mr. Kennedy announced on social media that Covid vaccines would no longer be recommended for healthy children or pregnant women.
The medical organizations had asked the court to restore the immunization schedule from a year ago, before Mr. Kennedy began making revisions.
The goal is “to stop dangerous vaccine policies and to restore science to our nation’s vaccine decision making,” said Mark Del Monte, chief executive of the American Academy of Pediatrics.
The pediatrics academy lauded the court’s ruling on Monday, saying it “effectively means that a science-based process for developing immunization recommendations is not to be trifled with and represents a critical step to restoring scientific decision-making to federal vaccine policy that has kept children healthy for years.”
The lawsuit addressed a series of changes made by Mr. Kennedy and his associates over the last year. In June, Mr. Kennedy fired all 17 previous members of the vaccine committee and selected new panelists, most of whom shared his skepticism of vaccines and mandates.
In three meetings since then, the panelists rescinded several recommendations for childhood shots, including the immunization of all newborns against hepatitis B, a highly infectious virus that can severely damage the liver.
Separately, Jim O’Neill, whom Mr. Kennedy had installed as the C.D.C.’s acting director at the time, announced a new schedule for childhood vaccines in January that rescinded recommendations for some shots, effectively reducing the number of diseases against which children are routinely immunized to 11 from 17.
Mr. O’Neill and other federal officials said mistrust in vaccines had led to declining immunization rates and argued that the truncated schedule would restore the public’s faith. The shots dropped from the routine schedule would still be available after consultation with a doctor.
The revision of the schedule bypassed the vaccine panel entirely. Changes to the vaccination schedule are typically made by the vaccination committee after a careful review of the benefits and potential risks, in a process that can take months or years, said Dr. Giridhar Mallya, a senior policy officer at the Robert Wood Johnson Foundation, which supports universal health care.
“We cannot say the same for the changes that were made to the vaccine schedule just in the past year,” Dr. Mallya said.
After the lawsuit was filed last summer, it was expanded to include the additional vaccine developments, with the medical organizations asking the court to throw out the revisions to the schedule. The suit also gained supporters: An amicus brief representing more than 100 public health experts and organizations, including the Robert Wood Johnson Foundation, was filed in February.
“We really see vaccines, particularly childhood vaccines, in this nation as a true crown jewel of public health,” Dr. Mallya said. “Seeing a set of drastic, arbitrary and poorly reasoned changes to those recommendations is of real concern to us.”
Judge Murphy seemed to agree with that assessment.
“It is undisputed that Director O’Neill issued the January 2026 Memo without sufficiently consulting A.C.I.P.,” he wrote in his decision. “Therefore, he lacked authority to issue the January 2026 Memo and, in so doing, acted contrary to law.”
“The C.D.C. cannot simply bypass A.C.I.P. in altering the immunization schedules,” he added.
Many of the members Mr. Kennedy appointed are physicians, but unlike previous panelists, they have little to no expertise in vaccines or immunology.
Last month, the vaccine panel’s chair, Dr. Kirk Milhoan, a pediatric cardiologist, suggested that all childhood vaccines, including the shots against polio and measles, should be optional, because the diseases no longer pose the dangers they once did — a position most public health experts immediately denounced as dangerous.
Other committee members have suggested, contrary to the scientific consensus, that Covid shots are deadly, and should be taken off the market.
Allowing the panelists to make decisions about vaccines is “just as reckless as letting a group of amateur pilots dictate how our airplanes should fly,” said Dr. Tina Hartert, a co-chair of the American Thoracic Society’s vaccine advisory committee. “The stakes in both scenarios are life and death,” Dr. Hartert said. The thoracic society joined the amicus brief.
“The medical and scientific backlash against this hasn’t changed anything, so I think it really is going to take some critical legal defense to protect the health of our nation,” she added.
The pediatrics academy and many other organizations, including the American Medical Association, have banded together to provide the public with information and evidence that would normally be offered by the vaccine panel and by the Centers for Disease Control and Prevention.
Last month, the pediatrics academy issued its own new immunization schedule, which largely mirrors the previous C.D.C. vaccination schedule. Most physicians’ groups, states and insurance companies have also committed to following the previous schedule.
“We would prefer to be collaborating with federal health officials instead of appearing in a courtroom to challenge their actions,” Mr. Del Monte, the pediatrics academy’s chief executive, said.
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Apoorva Mandavilli reports on science and global health for The Times, with a focus on infectious diseases and pandemics and the public health agencies that try to manage them.
