The Trump administration has canceled funding for dozens of studies seeking new vaccines and treatments for Covid-19 and other pathogens that may cause future pandemics.

The government’s rationale is that the Covid pandemic has ended, which “provides cause to terminate Covid-related grant funds,” according to an internal N.I.H. document viewed by The New York Times.

But the research was not just about Covid. Nine of the terminated awards funded centers conducting research on antiviral drugs to combat so-called priority pathogens that could give rise to entirely new pandemics.

“This includes the antiviral projects designed to cover a wide range of families that could cause outbreaks or pandemics,” said one senior N.I.H. official who spoke on condition of anonymity for fear of retaliation.

The vaccine research also was not focused on Covid, but rather on other coronaviruses that one day might jump from animals to humans.

Describing all the research as Covid-related is “a complete inaccuracy and simply a way to defund infectious disease research,” the official said. Robert F. Kennedy Jr., the health secretary, has said that the N.I.H. is too focused on infectious diseases, the official noted.

The funding halts were first reported by Science and Nature. The cancellations stunned scientists who had depended on the government’s support.

“The idea that we don’t need further research to learn how to treat health problems caused by coronaviruses and prevent future pandemics because ‘Covid-19 is over’ is absurd,” said Pamela Bjorkman, a structural biologist at Caltech who had been studying new vaccines.

The goal of the projects was to have vaccines and drugs ready if a new pandemic hit, rather than spending precious months developing them from scratch.

“In the last pandemic, we really were caught with our pants down,” said Paul Bieniasz, a virologist at Rockefeller University who was collaborating with Dr. Bjorkman.

“And if we don’t learn that lesson and prepare better for the next pandemic, we are unlikely to do better than we did last time.”

Dr. Bieniasz, Dr. Bjorkman and their colleagues were developing a vaccine that might protect against a wide range of coronavirus species.

The researchers discovered new strategies to coax the immune system to learn how to recognize molecular features common to more than just one type of virus. Results from animal experiments were promising.

But now, with their funds abruptly cut, the scientists said they doubted they could build on those results. Dr. Bieniasz said that the termination had left him “angry, disappointed, frustrated.”

Other scientists had been working on antiviral treatments, part of a program started in 2021.

With $577 million in support from the N.I.H., a nationwide network of labs had been studying how viruses replicate, and then searching for drugs that could block them.

The researchers focused on viral families that include some of the most worrisome pathogens known, such as Ebola and Nipah virus. Scientists had discovered a number of promising molecules and were advancing toward clinical trials.

Reuben Harris, a molecular virologist at UT Health San Antonio, said that the promising compounds uncovered by the program included an antiviral drug that stops Ebola and related viruses from entering cells.

“It could be deployed to help a lot of people fast,” Dr. Harris said.

It looked as if some compounds might work against a number of virus families. “It’s some of the most exciting science I’ve seen in my career,” said Nevan Krogan, a systems biologist at the University of California, San Francisco.

On Wednesday morning, Dr. Krogan and dozens of his colleagues gathered in a campus meeting room to review those results. And they also discussed what, if anything, they could do now.

“One student asked me, ‘Well, I have an experiment booked on this microscope tomorrow — can I do it?’” Dr. Krogan said. “And I’m like, ‘Well, I don’t know.’”

Dr. Harris said that, without ongoing support, the promising drugs he and others had found would not move into clinical trials. “It’s tragic — I don’t have too many words to describe that right now,” he said.

In 2023, Mr. Kennedy said that he wanted to take “a break” from infectious disease research to focus instead on chronic disease.

Jason McLellan, a virologist at the University of Texas at Austin who worked on the antiviral program, saw the cancellations of pandemic research as following through on that promise.

Dr. McLellan, whose earlier research was fundamental to the creation of Covid vaccines in 2020, said this week’s cuts made him wonder if he could continue studying pandemics in the United States.

“We’ve had conversations and are beginning to put plans into motion to gather more information,” he said, referring to the possibility of moving abroad.

“My lab is a structural virology lab that focuses on structure-based vaccine design,” he added. “If the focus is on chronic diseases, that doesn’t leave much funding for us.”