Six leading medical organizations filed a lawsuit on Monday against Robert F. Kennedy Jr., the health secretary, and the federal Department of Health and Human Services, charging that recent decisions limiting access to vaccines were unscientific and harmful to the public.

The suit, filed in federal court in western Massachusetts, seeks to restore Covid vaccines to the list of recommended immunizations for healthy children and pregnant women.

Mr. Kennedy has been on a “decades-long mission” to undermine vaccines and to portray them as more dangerous than the illnesses they are designed to prevent, said Richard H. Hughes IV, a lawyer who teaches vaccine law at George Washington University and is leading the effort.

“The secretary’s intentions are clear,” Mr. Hughes said: “He aims to destroy vaccines.”

The H.H.S. did not immediately respond to a request for comment.

The plaintiffs include the American Public Health Association, the American Academy of Pediatrics, the Infectious Diseases Society of America, the American College of Physicians, the Society for Maternal-Fetal Medicine and the Massachusetts Public Health Alliance.

The groups are joined by a pregnant woman, identified only as Jane Doe, who said she was unable to get a Covid shot.

In May, Mr. Kennedy announced in a video posted on X that the Centers for Disease Control and Prevention would stop recommending Covid vaccines for healthy children and pregnant women.

Mr. Kennedy’s decision contravenes years of evidence showing that pregnant women are at higher risk of severe illness, miscarriage and stillbirth if they contract Covid, public health experts said.

“From a scientific perspective, a pregnant woman, by her very nature, is immunocompromised,” said Georges Benjamin, executive director of the American Public Health Association.

Mr. Kennedy’s decision “didn’t follow the normal process,” Dr. Benjamin added.

Normally, scientific advisers to the C.D.C. would debate the research and make recommendations to the agency’s director. Mr. Kennedy made the announcement without consulting C.D.C. staff or its independent advisers.

The secretary and his associates have also ignored statements from professional organizations, Dr. Benjamin said.

“This is not a group that follows advice, it’s not a group that responds to political pressure, but so far, they respond to legal pressure,” he added.

Although the lawsuit focuses on access to Covid vaccines — the only recommendation for which the plaintiffs believed they were able to demonstrate harm — more vaccine decisions may be added.

Mr. Kennedy and the people he has installed in key roles in the administration have also said they may limit Covid vaccines only to older adults and people with certain health conditions, unless the manufacturers provide new evidence of effectiveness.

New C.D.C. advisers appointed by Mr. Kennedy have withdrawn support for multidose flu vaccines that contain thimerosal, a mercury-based preservative that the anti-vaccine community has long falsely contended is dangerous to children.

And they have said they will scrutinize childhood and adolescent immunization schedules, including the number of doses that American children receive.

“Pediatricians are alarmed as experts are sidelined, evidence is dismissed, and vaccine infrastructure is undermined while misinformation spreads,” said Dr. Susan J. Kressly, president of the pediatrics academy. “These actions endanger children and erode public confidence in lifesaving vaccines.”

The individual complainant, Jane Doe, is a physician at a hospital who is more than 20 weeks pregnant, and whose work puts her at increased risk of exposure to Covid.

The suit describes Mr. Kennedy’s various efforts to undermine vaccines, including promoting theories that were debunked long ago but remain popular with anti-vaccine groups.

It also claims that Mr. Kennedy’s policies have fueled unfounded fears about vaccine safety that are making it more difficult for doctors to treat and counsel their patients.

In June, Mr. Kennedy fired all 17 experts on the C.D.C.’s vaccine advisory panel. Insurance companies and government programs like Medicaid are required to cover shots recommended by the panel, called the Advisory Committee on Immunization Practices.

Mr. Kennedy then appointed eight new committee members, at least half of whom had expressed strong skepticism about some vaccines. One member withdrew from the committee the evening before its first meeting in late June because he was unable to divest himself of financial conflicts of interest.

Breaking with decades of tradition, the pediatrics academy boycotted the meeting, saying, “We won’t lend our name or our expertise to a system that is being politicized at the expense of children’s health.”

The new lawsuit asks the court to order Mr. Kennedy to reinstate Covid vaccines in the immunization schedules.

“The secretary’s authority needs to have some scientific and procedural basis for the decisions that he makes,” Dr. Benjamin said. “Otherwise, we have someone practicing medicine without a license and people will be harmed.”