The Trump administration is threatening to cut tens of millions of dollars in federal funding for Columbia University, making the school the first major target in its effort to root out what it considers antisemitic harassment on college campuses.

A comprehensive review of Columbia University’s federal contracts and grants was announced Monday night, shortly after Linda McMahon was confirmed as the secretary of education in a party-line vote.

The review, which will be led by the Department of Health and Human Services, the Department of Education and the General Services Administration, has already identified $51.4 million in contracts between Columbia and the federal government that could be subject to stop-work orders. Health and Human Services said in a news release that the review was necessary “given Columbia’s ongoing inaction in the face of relentless harassment of Jewish students.”

Far more could be on the line: A federal task force will conduct a comprehensive review of the “more than $5 billion in federal grant commitments to Columbia University to ensure that the university is in compliance with federal regulations, including its civil rights responsibilities,” the news release said.

Much of that money flows through Columbia’s Irving Medical Center, one of the largest academic medical centers in the country. In announcing the review, Robert F. Kennedy Jr., the new health secretary, said in a statement that “antisemitism — like racism — is a spiritual and moral malady that sickens societies and kills people with lethalities comparable to history’s most deadly plagues.”

More than a quarter of Columbia’s $6.6 billion in annual operating revenue comes from federal sources, according to its 2024 financial statements. Of that, about $1.3 billion comes from federal research grants, the category of revenue most immediately at risk from this review.

The National Institutes of Health gives the most federal research money to Columbia, providing $747 million in 2023. An additional $206 million came from other Health and Human Services programs.

Columbia said in a statement Monday evening that it was reviewing the announcement and that it looked forward “to ongoing work with the new federal administration to fight antisemitism.”

The nation’s research universities stand to lose billions in federal funding because of Trump administration actions. For example, a new policy regarding overhead costs will have drastic effects on institutions that rely on N.I.H. grants. Under the new measure, the additional money that institutions get to offset overhead costs is capped at 15 percent of the total of the grant, instead of the 50 or 60 percent some universities receive. (That reduction is on hold because of a court decision.)

A letter to schools from the Department of Education also threatens to cut federal money to those that do not end diversity, equity and inclusion programs.

Columbia is additionally exposed to Trump administration pressure because of the prominence of its pro-Palestinian movement, whose tents overtook the university’s grassy quads last spring, giving rise to a wave of encampments nationally. The Trump administration considers many of the chants expressed at pro-Palestinian rallies, such as “From the river to the sea, Palestine will be free,” as antisemitic.

“Columbia is the only university named in all three investigations — a terrible trifecta — which leads us to the unappetizing conclusion that our alma mater will bear the brunt of whatever the Trump administration decides on,” said the Stand Columbia Society, a group of alumni that has been analyzing Columbia’s financial exposure to the Trump administration’s moves.

Dozens of pro-Palestinian Columbia students were arrested last spring after participating in the encampments and the takeover of Hamilton Hall, a campus building. But the disciplinary process is ongoing in most of these cases, and no expulsions have been announced. On Tuesday, a Columbia official, speaking on background to discuss student disciplinary matters, said that four students had already been suspended in connection with behavior related to Hamilton Hall and the encampments and that other cases were expected to be concluded shortly.

The loss of federal grant funding would be devastating, said Gil Zussman, a professor of electrical engineering at Columbia who has been calling for Columbia to take more aggressive action to protect Jewish and Israeli students from protesters who break rules.

“This crisis should be used by the Columbia leadership to make immediate changes related to enhancing and enforcing the university rules, despite objections from a vocal minority of faculty, most of whom do not rely on federal funding for research,” Dr. Zussman said.

Dr. Brent Stockwell, the chair of the department of biological sciences, said that threatening research funding was exactly the wrong lever for the Trump administration to pull to fight antisemitism, in part because many Jewish faculty members will lose their jobs if their funding is eliminated.

“They just don’t understand that if they wipe out all the Jewish researchers who are doing frontier, cutting-edge research, that will just make things more difficult,” said Dr. Stockwell, who is Jewish. “It’s adding salt into the wound.”

Representative Tim Walberg, the Republican chairman of the House Education and Work Force Committee, wrote in a Monday news release, “For more than a year, Columbia’s leaders have made public and private promises to Jewish students, faculty, and members of Congress that the university would take the steps necessary to combat the rampant antisemitism on Columbia’s campus. Columbia has failed to uphold its commitments, and this is unacceptable.”

Writing on Truth Social on Tuesday morning, President Trump underscored his stance regarding what he considered the appropriate penalty for pro-Palestinian demonstrators who take over a building and cause injury or property damage.

“All Federal Funding will STOP for any College, School, or University that allows illegal protests,” Trump wrote. “Agitators will be imprisoned/or permanently sent back to the country from which they came. American students will be permanently expelled or, depending on on the crime, arrested. NO MASKS!”