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The Defense Department’s vaunted network of research laboratories — whose scientists helped develop satellite communication, radar technology, and even the computer mouse — was in trouble.

The labs lost a significant share of their staff last year, largely in response to the Trump administration’s efforts to thin the federal work force, the report found. Refilling critical positions was proving difficult due in part to President Trump’s demand that new hires be screened for their loyalty to his goals. The report, issued by the Pentagon, pointed to “potentially grave consequences for the future of national defense.”

The turmoil inside scientific research has extended beyond the Pentagon. The Energy Department, a key hub of nuclear and quantum research, has lost more than 1,000 scientists and technical staff. The National Science Foundation, for decades a primary backer of long-term, foundational research, has withheld more than $1 billion in funding. And at the National Institutes of Health, the biggest funder of medical research, officials delayed or canceled more than 2,000 grants to biomedical researchers focused on topics such as Alzheimer’s, cancer and other diseases.

Under Mr. Trump, the federal government is still spending roughly as much on research — about $200 billion this year — as the administrations that came before. Scientists across the country are still receiving grants; universities are still being funded. But beneath the surface, the system of federally funded science that helped make the United States a global superpower is under intense strain from Trump policies, jeopardizing the nation’s advantages in defense, medicine and technology, a New York Times examination has found.

The damage is the byproduct of three pillars of Mr. Trump’s broader agenda.

One is the sweeping job cuts and grant cancellations engineered last year by the so-called Department of Government Efficiency, the Elon Musk-led effort that viewed much of federal spending as wasteful and whose effects are still reverberating across the bureaucracy.

A second is the administration’s continued pressure on research universities, in which the White House used funding cuts to push schools into adhering to its demands for ideologically driven policy shifts.

The third is a campaign by Mr. Trump’s budget director, Russell T. Vought, to impose more political control over how the government spends money appropriated by Congress, further infusing politics into decisions around scientific research.

If not for the courts curbing the administration’s campaign against universities and lawmakers in both parties rejecting cuts to research funding, the impact on science would have been far deeper. Still, the effects of the broader agenda have rippled through nearly every facet of the nation’s research machine.

Aspiring scientists have seen their career paths thwarted, with fewer available spots for Ph.D. students. The number of Ph.D. applications from foreign students, typically a significant share of U.S. science programs, shrank by 21 percent this year at leading universities, according to data gathered for the Association of American Universities. Total Ph.D. admissions at those schools have dropped as universities try to make do with less resources.

Even the agencies working on topics that Mr. Trump and his aides have called priorities — including national defense, artificial intelligence, quantum computing and nuclear energy — have been depleted.

By many measures, China is closing the gap with the United States as the world’s research leader. Some organizations that rank global universities show China’s best schools increasingly displacing American universities at the top. And the impact of Chinese research papers, as measured by citations from other scientists, has caught up with the United States, according to Clarivate, a data and analytics company.

By the time the full consequences of the administration’s actions become apparent, experts warn, it could be too late to fix. That’s because basic research funded by federal grants often takes decades to mature into the technology, medical treatments and consumer products that change American life.

DOGE and the White House directed agencies to search for terms in grant descriptions that might reveal science the administration viewed as liberal, including anything that appeared to promote diversity, equity and inclusion.

The cuts cascaded through the country.

Ann D. Cohen, a neuroscientist who co-directs an Alzheimer’s research center at the University of Pittsburgh, had been working on a five-year study looking at how people’s exposure to stress and health problems earlier in life can affect their odds of developing the disease.

The research was critical to developing better treatments and health interventions, Dr. Cohen said. “If the triggering event is poor cardiovascular health in midlife, we can actually deploy public health strategies to improve those things, and potentially have an effect on Alzheimer’s,” she said.

Recruiting people from different backgrounds was difficult, because people who volunteer for scientific studies tend to have higher than average incomes and education levels. So Dr. Cohen and her colleagues recruited from rural Western Pennsylvania, whose residents were more likely to be white and low-income, as well as from Black communities in Pittsburgh.