The Trump administration’s moves to freeze federal funding to universities have targeted elite institutions, like Harvard and Columbia. But many other schools are concerned that the administration’s policies threaten the future of research and development programs.

In fiscal year 2023 alone, roughly $60 billion flowed from the federal government to universities in all 50 states, funding research on an array of topics, like cancer, Alzheimer’s disease and rare isotope beams. Funding went to small colleges, like the College of St. Benedict in Minnesota, as well as major public and private research institutions, like Georgia Tech and Johns Hopkins. That money, in turn, often provided a boon to the surrounding communities.

More federal research and development money generally flows to locations with bigger populations that are home to multiple major universities, like Chicago, Los Angeles and big East Coast cities. But institutions in less populated states, like the University of Utah and the University of Kansas, also receive hundreds of millions of dollars.

Some of that funding is now on the chopping block as the administration seeks to exert control over universities, and as Elon Musk’s initiative, known as the Department of Government Efficiency, moves to root out what it says is wasteful spending. The government’s cuts to the National Institutes of Health have hit research and development funding particularly hard, leaving some schools unsure about the future of certain projects.

Many of the 60-plus schools that the Trump administration has accused of antisemitism and threatened to investigate are major recipients of federal research and development money. Collectively, those schools spent about $23 billion in federal research money in fiscal year 2023, more than one third of the total amount distributed to universities.

The funding system grew out of World War II and the Cold War, when the U.S. government began paying universities huge sums to help it build more powerful bombs and win the space race against the Soviet Union. It has now become one of the few drivers of innovation that is widely distributed across the country, said Joseph Parilla, a senior fellow at Brookings Metro, a division of the Brookings Institution, the think tank in Washington.

“For a lot of places it is the last remaining economic and innovation engine that gives them relevance in a modern, technology-driven economy,” Mr. Parilla said of federal research and development funding.

The threats to this funding are concerning enough that community and Mississippi State University leaders in Starkville, one of the smallest cities in the Southeast with a major research institution, have been discussing the potential consequences. The university’s research has led to economic growth in the state and helped bring several aerospace companies to the area. In fiscal year 2023, the school spent more than $150 million in federal research funding.

It remains to be seen which programs might be affected by cuts, and what it might mean in turn for Starkville. Already, an aquaculture research project at the university intended to improve food security in Africa and Asia, which was funded by the U.S. Agency for International Development, has been paused.

“Every time you touch the university, you, in effect, touch Starkville,” said the city’s mayor, Lynn Spruill, a Democrat.

Federal funding has a big effect on larger economies, too, university leaders say. Stanford and the University of California, Berkeley, are essential to Silicon Valley, for example, and Boston’s biotech industry is closely tied to its universities, like the Massachusetts Institute of Technology.

The biggest public recipient of federal funding, the University of Washington, in Seattle, spent nearly $1.2 billion in fiscal year 2023, with large amounts coming from the Department of Health and Human Services, the Department of Defense and the National Science Foundation. The funds accounted for roughly 70 percent of the school’s research expenditures. The university was among the schools notified by the Trump administration that they could face penalties after pending investigations into antisemitism.

The university’s research projects touch Washington’s seafood industry, aerospace manufacturing and the military, said Mari Ostendorf, the university’s vice provost for research. Many projects require buy-in from community members. Fisheries research, she said, relies on fishermen to help guide inquiries and make sure findings are useful.

The university has also been waiting to find out if its Alzheimer’s disease research center will receive another $22 million grant, distributed over five years, from the N.I.H., said Shelly Sakiyama-Elbert, the vice dean for research and graduate education at the university’s School of Medicine. Dr. Sakiyama-Elbert said she had expected to learn by February if she could expect the grant to be renewed. The current one is set to run out on Wednesday.