After decades of partnership with the U.S. government, colleges are facing new doubts about the future of their federal funding.

President Donald Trump’s administration has been using the funding spigot to seek compliance with his agenda, cutting off money to schools including Columbia University and the University of Pennsylvania. All the while, universities across the country are navigating cuts to grants for research institutions.

The squeeze on higher education underscores how much American colleges depend on the federal government — a provider of grants and contracts that have amounted to close to half the total revenue of some research universities, according to an Associated Press analysis.

It adds up to a crisis for universities, and a problem for the country as a whole, say school administrators and advocates for academic freedom. America’s scientific and medical research capabilities are tightly entwined with its universities as part of a compact that started after World War II to develop national expertise and knowledge.

“It feels like any day, any university could step out of line in some way and then have all of their funding pulled,” said Jonathan Friedman, managing director of free expression programs at PEN America.

Tens of billions of

dollars are at stake

The AP analysis looked at federal funding for nearly 100 colleges currently under investigation for programs the administration has deemed as illegally pushing diversity, equity and inclusion, or for not doing enough to combat antisemitism. Those schools took in over $33 billion in federal revenue in the 2022-2023 academic year. That’s before taking into account federal student aid, which represents billions more in tuition and room-and-board payments.

For most of the schools, around 10% to 13% of their revenue came from federal contracts or research funding, according to the analysis. For some prestigious research universities, however, federal money represented up to half of their revenue.

The AP analyzed data from the National Center for Education Statistics and federal audit reports, with help from researchers Jason Cohn and James Carter at the Urban Institute.

Perhaps no school is more vulnerable than Johns Hopkins University, which received $4 billion in federal funds, close to 40% of its revenue, according to the analysis. Much of that went to defense research, paying for projects like missile design, submarine technology and precision tracking systems in outer space. Billions of dollars also went to medical research for topics such as immunology and transplants, aging, neuroscience and mental health.

Johns Hopkins is facing an antisemitism investigation, which threatens its federal money, but already it has been feeling the effects of cuts to research grants from the National Institutes of Health and other federal agencies. Earlier this month, it announced 2,200 layoffs.

“We face challenging times for the patients and families that rely on us for cures and treatments, and for the researchers dedicated to the pursuit of improving the health of all Americans,” the university said in a statement.

Trump extracted concessions

from Columbia

Trump has singled out Columbia University, making an example of the Ivy League school by withholding $400 million in federal money. The administration repeatedly accused Columbia of letting antisemitism go unchecked at protests against Israel that began at the New York City university last spring and quickly spread to other campuses — a characterization disputed by those involved in the demonstrations.

As a precondition for restoring that money — along with billions more in future grants — the Republican administration demanded unprecedented changes in university policy. Columbia’s decision last week to bow to those demands, in part to salvage ongoing research projects at its labs and medical center, has been criticized by some faculty and free speech groups as capitulating to an intrusion on academic freedom.