Officials at the Food and Drug Administration have blocked publication of several studies supporting the safety of widely used vaccines against Covid-19 and shingles in recent months, a spokesman for the Department of Health and Human Services confirmed.

The studies, which cost millions of dollars in public funds, were conducted by scientists at the agency, who worked with data firms to analyze millions of patient records. They found serious side effects to be very rare.

In October, the scientists were directed to withdraw two Covid-19 vaccine studies that had been accepted for publication in medical journals. In February, top F.D.A. officials did not sign off on submitting abstracts about studies of Shingrix, a shingles vaccine, to a major drug safety conference.

The withdrawal of the studies is the latest step by the administration to try to limit access to vaccines. It has sharply cut research funding for vaccine development, released unvetted information casting doubt on vaccines, and blocked other information supporting their safety, most recently a paper on Covid vaccine effectiveness by career scientists from the Centers for Disease Control and Prevention.

Asked about the withdrawal of the Covid vaccine safety studies, Andrew Nixon, a spokesman for the Department of Health and Human Services, said in an email: “The studies were withdrawn because the authors drew broad conclusions that were not supported by the underlying data. The F.D.A. acted to protect the integrity of its scientific process and ensure that any work associated with the agency meets its high standards.”

Of the shingles study that found the vaccine to be effective, he said, “The design of that study fell outside the agency’s purview.” He did not address a question about the Shingrix safety study, which found the vaccine to be safe.

A senior administration official said the decisions about the research had not reached Dr. Marty Makary, the F.D.A. commissioner, or Health Secretary Robert F. Kennedy Jr. Dr. Vinay Prasad was the head of the F.D.A. vaccine office at the time. Dr. Prasad, who recently left the agency, did not respond to a request for comment.

Last June, Mr. Kennedy’s office asked career C.D.C. staff members to delete from the agency’s website a 17-page summary supporting the safety of thimerosal, an additive largely removed from vaccines 25 years ago. Career scientists were later called into Health and Human Services legal offices and grilled about how the summary had been posted in the first place, they previously told The New York Times.

In posts on a website and on social media in August, Mr. Kennedy called for a prominent journal to “immediately retract” a large Danish study concluding that the vaccine additive aluminum salts was safe. Dr. Christine Laine, the editor in chief of the journal, Annals of Internal Medicine, said Mr. Kennedy did not directly contact the journal seeking a retraction. The study was not retracted.

In recent weeks, Dr. Jay Bhattacharya, who was serving as interim leader of the C.D.C., canceled the publication of a report concluding that the Covid vaccine sharply cut the odds of hospitalizations and emergency room visits last winter, saying the study had limitations.

“At a moment when public trust in institutions like the C.D.C. is fragile, we cannot afford to lower our standards,” Dr. Bhattacharya wrote in an editorial about news coverage of his decision.

Dr. Aaron S. Kesselheim, a Harvard University medical professor who studies F.D.A. regulation, said he had worked with the agency on a number of research papers and found its work to meet “the highest standards of scientific investigation.” He suggested that the request to pull the papers was an act of “censorship.”

He added: “At any other time in history, this would be a major scandal that would lead to congressional hearings and resignations of leadership, and I hope that’s what happens next.”

The withdrawn F.D.A. studies examined the safety of the Covid vaccines used in 2023 and 2024. The agency’s scientists worked with outside data firms that compile and analyze massive data sets under contracts that cost taxpayers millions of dollars each year.

Both studies saw some light of day before they were pulled from publication. One, which examined the Covid vaccine in people older than 65, was posted on a preprint server, which is a repository for studies that have not yet undergone peer review. The study reviewed the records of about 7.5 million Medicare beneficiaries who got the vaccine. The researchers focused on the period of about 21 days after they got the vaccine and compared it to the next 20 days. They were looking to see if there were more health problems in the period right after vaccination.

The study looked at 14 health outcomes potentially caused by the vaccine, including heart attacks, strokes and Guillain-Barré syndrome, an autoimmune condition sometimes associated with vaccines.

They only found a concern with one outcome, anaphylaxis, a severe allergic reaction affecting about 1 in a million people, from the Pfizer vaccine. “No other statistically significant elevations in risk were observed,” the study said.

The study was withdrawn after it had been accepted by the peer reviewed journal Drug Safety, according to people familiar with the work. Michael Stacey, a spokesman for the journal, said it deems submissions to be confidential and would not comment on them.

The Times obtained a copy of the Covid vaccine safety study of people who were 6 months to 64 years old. An abstract of the study appeared at one conference and remains online. Its withdrawal was first reported by STAT News.

That study examined the records of 4.2 million Covid vaccine recipients and examined their later experience with 17 conditions, including swelling of the brain, major blood clots, stroke and heart attacks. The study found rare cases of fever-related seizures and myocarditis, or inflammation of the heart muscle, known to be associated with Covid vaccines.

“Given the available evidence, F.D.A. continues to conclude the benefits of vaccination outweigh the risks,” the study said.

Angela Rasmussen, an editor in chief of the journal Vaccine, said the paper had been withdrawn by the authors.

Dr. Caleb Alexander, a drug safety and methodology expert at Johns Hopkins University, reviewed both studies at the request of The Times and said that “no study answers every question” but “there is nothing inherently problematic regarding these reports.”

“It’s too bad that these haven’t seen the full light of day,” Dr. Alexander said in an email. “They provide useful information regarding the most commonly used COVID-19 vaccines.”

Jeffrey Morris, director of the University of Pennsylvania biostatistics division, who also reviewed the study drafts at the request of The Times, said the studies were generally well done.

“I think if there’s any critique,” he said, “it’s that they don’t do enough of these studies with the resources they have.”

Dr. Jeanne Marrazzo, a former high-ranking National Institutes of Health official and chief executive of the Infectious Diseases Society of America, said that F.D.A. leaders withdrawing papers from publication is a “pretty active act of sabotage.”

“This black box of decision making around data suppression should be having people very alarmed and very worried,” said Dr. Marrazzo. She filed a whistle-blower complaint against the N.I.H., was fired by Mr. Kennedy and has since sued the agency, claiming that she was ousted for objecting to its policies.

By contrast, Mr. Kennedy’s team has had lower standards for releasing information critical of vaccines. A memo by Dr. Prasad, the former head of the F.D.A.’s vaccine division, drew widespread news coverage by claiming that the Covid vaccine had been linked to the deaths of 10 children, a conclusion the agency has not backed up or explained.

In February, agency officials did not sign off in time for staff to submit abstracts on two studies of the Shingrix vaccine to a drug safety conference, according to two people familiar with the decision. A senior administration official said the studies were not moving forward at the agency.

One study found the efficacy to be in line with findings from the clinical trials done before agency approval. A safety study also aligned with what was known, finding an elevated but low risk for Guillain-Barré syndrome, an autoimmune disease already noted in the vaccine’s label.

Dr. Helen Chu, an infectious disease doctor who was among 17 scientists fired from an influential vaccine advisory body at the C.D.C. last summer, said large studies by health agencies are closely watched by doctors and professional societies. They are important, she said, because they can examine the effect of a vaccine on millions of people, far more than the thousands that were tracked in clinical trials.

“You really do need these studies for us to truly be safe and to make sure that vaccines continue to be safe,” she said. “These types of studies have to be done and the results have to be published.”