When President Bill Clinton worked with a bipartisan Congress to enact a federal program to guarantee vaccines for poor children, they agreed that the authority over buying shots from drug makers should rest with the health secretary. The bill’s drafters did not consider that an extremely vocal critic of childhood vaccines would emerge as a nominee for the role.

That critic, Robert F. Kennedy Jr., comes before the Senate for confirmation hearings this week. If confirmed, he would have the power to limit or even cut off contracts with the makers of vaccines for more than half the nation’s children under the $8 billion dollar Vaccines for Children program.

The program has been credited with raising national vaccination rates and protects nearly 38 million low-income and working-class children from diseases like polio, measles, whooping cough and chickenpox.

Mr. Kennedy has said he would not take vaccines away from anyone, but he has a long history of questioning vaccine safety. The far-reaching authority he would wield over vaccine policy has become increasingly worrisome for public health experts, researchers and lawmakers from both parties.

Some architects of the program are trying to persuade senators to oppose his nomination.

“I think he’s dangerous to children’s health,” Donna E. Shalala, Mr. Clinton’s health secretary and a former Democratic congresswoman, said in an interview. She said she had spoken to Republican senators who expressed uneasiness about Mr. Kennedy, but would not name them.

Confirmation hearings for Mr. Kennedy will begin on Wednesday before the Senate Finance Committee, and continue on Thursday before the Senate Health, Education, Labor and Pensions Committee. The back-to-back sessions will give senators of both parties an opportunity to ask Mr. Kennedy pointed questions about how he would oversee the nation’s large health agencies and vaccine policies.

Lawmakers have already begun asking questions about what authority the health secretary would have over vaccines. At a round table on vaccine policy held by Senator Bernie Sanders, Independent of Vermont, last week, Senator Lisa Blunt Rochester, Democrat of Delaware, asked: “What are the protections and what are the ways that someone could come in and have an impact on reducing vaccines use?”

Experts told the senators that the authority included exerting power over vaccine approvals and using the prominent position possibly to raise fears or state things that are untrue.

A spokeswoman for Mr. Kennedy, Katie Miller, declined to respond directly to a question about Mr. Kennedy’s view of the children’s program.

For decades, Mr. Kennedy has sown doubts about the safety of vaccines and their ingredients. In 2021, he petitioned federal officials to revoke authorization of all coronavirus vaccines at a time when thousands of Americans were dying each week from Covid.

Mr. Kennedy has also worked for years on lawsuits claiming that Merck’s vaccine against HPV, a leading cause of cervical cancer, caused injuries. Records released in advance of the confirmation hearings also show that he plans to keep his financial stake in that vaccine litigation if he is confirmed.

His activism has made lawmakers in both parties uneasy. Several Republican senators, including Mitch McConnell of Kentucky, Lisa Murkowski of Alaska and Bill Cassidy of Louisiana, have suggested they are on the fence about how to vote.

Mr. McConnell, a polio survivor and former Republican leader, has said that anyone who engages in “efforts to undermine public confidence in proven cures” will face difficulty in getting Senate confirmation. Mr. Cassidy, a doctor and chairman of the HELP Committee, has not said how he will vote. Ms. Murkowski told CNN that she had concerns, adding, “Vaccines are important.”

The Vaccines for Children program was created in response to measles outbreaks that disproportionately affected poor children who could not afford vaccinations. It now protects against 19 diseases, according to the Centers for Disease Control and Prevention.

The law that established the program gives the health secretary power over contracts to buy millions of vaccine doses, including the authority to enter into, modify or decline the agreements. Drugmakers have delivered 71.5 billion doses to about 37,000 medical providers throughout the United States and its territories since the program’s inception.

Federal officials “control the whole means of supply and distribution,” according to Sara Rosenbaum, a professor emerita of health law and policy at George Washington University, who was asked by the Clinton administration to build the program.

“Who would have ever thought that it was a problem giving the secretary this kind of power?” she asked.

Some of the program’s defenders worry that just talking about the vaccines program might put it in jeopardy if Mr. Kennedy takes charge.

“Folks are very nervous about speaking these things out loud because they don’t want them to happen,” said Richard Hughes IV, a lawyer who represents vaccine makers and is a lecturer at George Washington University. “But these are things that could very well happen.”

Lawyers who specialize in vaccine policy pointed to other areas where the nation’s health secretary has authority over vaccines. One is the Vaccine Injury Compensation Program, which was set up in 1986 to shield vaccine makers from liability and to create a court system to compensate people harmed by vaccines.

Though Mr. Kennedy has suggested the liability shield provides incentives to vaccine makers to cut corners, he would not have authority to remove it — that lies with Congress. However, the health secretary can add injuries to a table of harms presumed to be caused by vaccines. The secretary can also add or remove vaccines from the court’s purview.

As an official above the Food and Drug Administration in the executive chain of command, the secretary could push the agency to pause or revoke the approval of established vaccines or to withhold approval from those seeking authorization.

“Those are real possibilities,” said Denise Hill, an Iowa lawyer who specializes in vaccine law. “And if you’d asked me five, 10 years ago, I would say it’s never going to happen, but now I can’t say that with any certainty.”

Ms. Hill said it would also be possible for the Trump administration to try to place conditions on the funds for the children’s vaccine program, such as dropping its mandate for students entering kindergarten to be immunized.

The secretary would also have the authority over an influential advisory panel at the C.D.C. called the Advisory Committee on Immunization Practices or A.C.I.P. The committee could be disbanded, according to Mr. Hughes. The secretary could also revisit vaccine-safety matters and reject the committee’s recommendations.

That committee tends to influence state-level policy, doctors and private insurers. But it has more direct authority over which vaccines are distributed by the children’s program. Dr. Walter Orenstein, who ran the C.D.C.’s immunization programs when the children’s program was started, said he was concerned that Mr. Kennedy could change the makeup of the committee.

“There is the potential that they could really put into the A.C.I.P. a substantial number of anti-vaccine people, and that would then have some potentially negative effects, in terms of changing current recommendations,” Dr. Orenstein said. “It could mean vaccines wouldn’t be provided through the Vaccines for Children program.”

Ms. Rosenbaum, who helped create the system, said Medicaid covered vaccines and the cost of administering them decades ago. But even so, many doctors did not want to go to the trouble to pay in advance to keep vaccines stocked in their offices.

Ms. Rosenbaum said the system they built was revolutionary in that it empowered the health secretary to negotiate prices with vaccine makers and have the doses shipped directly to thousands of providers.

The program has been expanded to cover working class families above the Medicaid income limits who rely on CHIP, or the Children’s Health Insurance Program. Those programs cover about 38 million infants, children and adolescents, including those who rely on Native American health systems.

Thirty years on, Ms. Rosenbaum said, as Mr. Kennedy faces confirmation, people familiar with the program have assumed it may be a target if he is confirmed. “People haven’t reacted with alarm for no reason,” she said.