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In Massachusetts, Moderna is pulling back on vaccine studies. In Texas, a small company canceled plans to build a factory that would have created new jobs manufacturing a technology used in vaccines. In San Diego, another manufacturing company laid off workers.

When Robert F. Kennedy Jr. was picked in November 2024 to become the next health secretary, public health experts worried that the longtime vaccine skeptic would wreak havoc on the fragile business of vaccine development.

Those fears are beginning to come true, according to executives and investors involved with companies that develop and sell vaccines and the technology that is best known for the Covid vaccines.

At conferences and in interviews, they described the emerging consequences of the Trump administration’s dismantling of the longstanding federal support for vaccines.

“There will be less invention, investment, and innovation in vaccines generally, across all the companies,” Dr. Stephen Hoge, the president of Moderna, said in an interview.

The Trump administration said it was not discouraging innovation.

But investors have grown hesitant to bet on a field that has fallen out of favor in Washington. Major manufacturers are reporting declining sales of their shots. Smaller companies are taking the brunt of the impact, with some stocks whipsawing in response to the changes.

Perhaps no vaccine maker has been hit harder by the federal policy changes than Moderna. Mr. Kennedy has repeatedly questioned the safety and effectiveness of the technology around which the company has built its business. The technology, known as messenger RNA, or mRNA, instructs the body to produce a fragment of a virus that then sets off an immune response. It can be more quickly tailored and manufactured compared to traditional approaches.

Last week, the Food and Drug Administration refused to review Moderna’s mRNA flu vaccine, saying its research design was flawed.

The health officials’ decisions are a striking departure from President Trump’s first term, when the federal government funded and shepherded Moderna’s Covid vaccine. The company’s stock price has plummeted more than 90 percent since its peak in August 2021, erasing about $180 billion in market value.

Pharmaceutical companies have dodged several of Mr. Trump’s threats, reaching favorable deals with the administration to avoid tariffs and keep prices high for most of the drugs they currently sell. But they have been unable to find common ground on vaccines.

“It’s a different world when you start discussing vaccines,” Albert Bourla, Pfizer’s chief executive, said last month. “There is almost like a religion there.” Asked what needs to change, Mr. Bourla said, “the health secretary.” Mr. Bourla also characterized Mr. Kennedy’s rhetoric as “anti-science.”

Mr. Bourla talks about the president with a different tone. He once said Mr. Trump deserved a Nobel Prize for championing the Covid vaccines.

Andrew Nixon, a spokesman for the Department of Health and Human Services, said, “We reject the claim that our approach to vaccines is anti-science or hostile to innovation.”

Mr. Kennedy has argued that Covid shots using mRNA are not effective because they do not prevent infection. He also once called them “the deadliest vaccine ever made.” Like all shots, mRNA vaccines sometimes cause side effects, but extensive research has found the shots are safe overall and that serious reactions occur rarely.

Under Mr. Kennedy’s leadership, the department has canceled contracts for mRNA technology, limited the use of Covid shots, and remade a crucial committee that recommends which vaccines Americans should take and when.

Last month, federal health officials overhauled the childhood vaccination schedule, reducing the number of recommended immunizations to 11 from 17, deciding that that the six vaccines that were dropped should now be given only in consultation with a clinician.

The changes “sent a chill through the entire industry,” said Jeff Coller, a scientist who works on mRNA at Johns Hopkins University. Dr. Coller advises several small mRNA companies and is on the executive committee of the Alliance for mRNA Medicines, a trade group.

Mr. Nixon defended the administration’s changes. “Vaccine policy at H.H.S. is guided by evidence-based science, public health outcomes and transparency, not by the business models or public statements of pharmaceutical executives,” he said.

So far, vaccine manufacturers say that they have no plans to exit the market and that their businesses are resilient enough to withstand the new pressures. Insurers have promised to continue to cover the vaccines that are no longer federally recommended, at least until the end of this year, promising to soften the financial blow for companies.

And despite increasing vaccine hesitancy, industry officials say they hope that Americans will be swayed by a vast body of research showing that vaccines save lives.

“Not everybody looks to the top of H.H.S. to get all of their guidance on how to live their lives,” Paul Hudson, the outgoing chief executive of Sanofi, told reporters last month. Still, he predicted a continued slowdown in vaccine sales because of “the misinformation that is going around.”

Sanofi recently halted early development of an mRNA flu vaccine, but said its decision was motivated by concerns about effectiveness, not politics.

Vaxcyte, a vaccine company near San Francisco, said last summer that it was pausing development of vaccines to protect against strep and the diarrhea-causing bacteria Shigella, attributing the decision to other priorities and a changing political and business climate.

Lost jobs for American workers

The federal vaccine policies, coupled with declining demand for Covid shots, have translated into hard times for Moderna.

Last year, the company laid off more than 800 workers, a tenth of its work force. It also lost more than $700 million in contracts to develop a shot to protect humans against bird flu after the Trump administration canceled the agreements. And the company shelved vaccines to protect against herpes, chickenpox, and shingles.

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Moderna says it plans to pull back on late-stage studies of some of its experimental vaccines. Credit…Brian Snyder/Reuters

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