For nearly 40 years, a special federal court system has compensated Americans who prove they were harmed by vaccines while also protecting the manufacturers from litigation.

Even the staunchest defenders of the Vaccine Injury Compensation Program agree it needs reform. It is slow, understaffed and can feel adversarial to families legitimately in need.

Now Health Secretary Robert F. Kennedy Jr. plans to overhaul the program, saying he will make it more efficient and speedier for Americans seeking payment.

He said in a social media post last month that the vaccine court had “devolved into a morass of inefficiency, favoritism and outright corruption.” Parents who believe their children were injured by vaccines are “facing the monumental power and bottomless pockets of the U.S. government,” he said.

Mr. Kennedy has also claimed, falsely, that the compensation program prevents families from suing vaccine makers in traditional courts. And he has claimed that the vaccine court punishes and intimidates expert witnesses and petitioners’ attorneys.

Experts fear that some of the changes Mr. Kennedy has hinted at could lead to an onslaught of lawsuits, jeopardizing the manufacture of vaccines and undermining their use.

“Kennedy can fix this system without burning it down,” said Tony Yang, a health policy expert at George Washington University. But Mr. Kennedy sounds “more like a frustrated lawyer who lost cases than an eager secretary trying to fix things.”

Indeed, allies of the secretary have fared poorly in the vaccine court. Their litigation in traditional courts — including a 2022 lawsuit in which Mr. Kennedy delivered closing arguments — also has fallen short.

The Department of Health and Human Services did not respond to repeated requests for comment.

Public health officials in the United States have been tracking vaccine safety for decades and have long said that shots routinely given to children are safe. But all vaccines have at least occasional side effects, and there are rare instances of serious injury.

Congress set up the vaccine court in 1986 after a spate of lawsuits began to drive vaccine makers out of the market. So-called special masters judge claims of injuries from vaccines, weighing the available evidence.

The program covers most routine immunizations given to children and pregnant women, and is funded by a small tax on each shot. The vaccine court has paid $5.4 billion in claims since its inception, awarding compensation in about 42 percent of the roughly 28,000 claims filed.

But in accordance with a great body of scientific evidence, the court’s special masters have denied thousands of claims that childhood vaccines are linked to autism. Mr. Kennedy, a prominent vaccine skeptic, believes that there is such a link and has long accused government officials of hiding the risks.

Some reforms widely seen as necessary would require Congress to intervene. Among them: more of the special masters who preside as judges over cases.

The legislation establishing the program allowed for three; five more were added later. But at least double that number are needed to adjudicate the roughly 1,200 applications each year, according to some experts.

The program also needs more staff to review medical records, and an online system for families to track the status of their claims. The compensation fund has a $4 billion surplus, some of which could be applied to remedy these problems.

Mr. Kennedy said in an interview last month that he wanted to ensure families seeking compensation “get it very quickly, and they get it without the kind of adversarial impediments that have now been erected over the past 40 years.”

A new fast-track system for rare injuries that studies have definitively linked to certain vaccines could speed up the process. In the current system, government lawyers sometimes fight families over settled links, said Altom Maglio, an attorney who has represented people in the vaccine court for 25 years.

“Fighting tooth and nail is just not appropriate, and doesn’t meet the goals,” he said.

At the same time, special masters sometimes make awards even when the connection between a side effect and vaccine is tenuous, said Dr. Daniel Salmon, director of the Institute for Vaccine Safety at Johns Hopkins Bloomberg School of Public Health.

“There are a lot of things that are being compensated where there’s inadequate evidence,” Dr. Salmon said. “We need more science.”

Mr. Kennedy has also suggested that injury claims regarding Covid-19 shots should be moved to the vaccine court. At present, those claims are piling up in a parallel federal system called the Countermeasures Injury Compensation Program.

Of more than 14,000 injury claims filed regarding Covid vaccines, only 69 have been paid out. More than 9,400 are pending, and about 4,800 have been dismissed.

Congress would need to act to move those claims to the Vaccine Injury Compensation Program. But adding the large Covid backlog to the vaccine court’s own poses huge challenges, Dr. Yang said: “You’re complaining about your kitchen sink, it’s clogged, and then you try to wash your bike in it.”

There are some aspects of the program that Mr. Kennedy can change without Congress. That includes altering the official table detailing the injuries presumed to be linked to certain vaccines.

Changing the table to say that certain vaccines cause autism or asthma, months or years after shots, for example, could hobble the system, opening the doors to tens of thousands of new claims that would previously have been dismissed.

“He’s talking about opening a can of worms that could result in Americans losing access to some vaccines and huge expenditures in court fees,” said Dr. Thomas R. Frieden, a former director of the Centers for Disease Control and Prevention.

Mr. Kennedy has said, falsely, that the vaccine court is the “exclusive remedy” for families seeking compensation. In fact, claimants can sue vaccine makers in traditional courts if the government does not respond to them within 240 days, or if they are dissatisfied with its offer of compensation.

But the traditional courts have not been any more generous to Americans who believe they were injured, said Renee Gentry, director of the Vaccine Injury Litigation Clinic at George Washington University.

“The idea that going to straight to civil litigation means you’re going to win is absurd,” Ms. Gentry said. “These are incredibly difficult cases.” She believes her clients are better off in the vaccine court.

Mr. Kennedy has been deeply involved in litigation over vaccines for years. For example, he worked on lawsuits against Merck over claims related to the Gardasil vaccine, which protects against the human papilloma virus.

As health secretary, Mr. Kennedy initially planned to keep his financial stake in the litigation. But he relinquished those earnings to an adult son following controversy at his confirmation hearing.

Senator Elizabeth Warren, Democrat of Massachusetts, also pressed him to pledge to refrain from suing pharmaceutical companies after he leaves government. “I’m not going to agree to that,” Mr. Kennedy said.

His harsh criticism of the program — and claims that it is corrupt — appear tied to his steadfast support to people who have lost in the court with unproven claims that vaccines cause autism, said Dorit Reiss, a law professor at the University of California, San Francisco, who has followed the cases.

Rolf Hazlehurst, who was until recently a lawyer with Children’s Health Defense, the anti-vaccine group Mr. Kennedy founded, has litigated his son’s case for 22 years, claiming that the measles vaccine and thimerosal, a preservative, caused his son’s autism.

The case has failed in forum after forum. Mr. Kennedy became involved in 2022, when claims were brought in a Tennessee court against the pediatrician who in 2001 inoculated Mr. Hazlehurst’s child.

Mr. Kennedy delivered the closing argument. The jury sided with the doctor.

Mr. Kennedy has also recently hired at H.H.S. — and has defended — David Geier, who has for years pushed the discredited theory that thimerosal caused autism.

Mr. Geier’s attempts to bill the vaccine court for his expertise regarding vaccine injuries were often challenged. One judge determined in 2016 that Mr. Geier’s report was “neither useful nor relevant, because he is not qualified as an expert concerning the matters he discusses.”

Mr. Kennedy also has hired another Children’s Health Defense alumna, Lyn Redwood, who presented inaccurate data that thimerosal caused autism at recent meeting of scientific advisers to the C.D.C.

The panelists, newly appointed by Mr. Kennedy, voted to withdraw endorsements of the few flu vaccines in which thimerosal is an ingredient.

Some experts are concerned that Mr. Kennedy may open the door to at least one proposal already pending in Congress — to abolish the Vaccine Injury Compensation Program altogether.

“I think he’s been really clear,” said Richard Hughes IV, a lawyer who represents vaccine makers. “He would be fine with the total collapse of the program.”