The Trump administration announced on Friday that it had canceled $400 million in federal grants and contracts to Columbia University, an extraordinary step that it said was necessary because of what it described as the school’s failure to protect Jewish students from harassment.

Columbia’s interim president, Katrina Armstrong, said in a universitywide email on Friday night that the school is taking the administration’s actions seriously. Columbia is “committed to working with the federal government to address their legitimate concerns,” she wrote.

The announcement escalated the administration’s targeting of Columbia, where protests last year over the war in Gaza set off a nationwide debate over free speech, campus policing and antisemitism, and led to similar demonstrations at schools nationwide.

The move also represents the latest in a series of attacks by Trump-aligned Republicans aimed at elite higher educational institutions, following last year’s congressional hearings that resulted in the departure of the presidents of Harvard and the University of Pennsylvania. It comes after recent executive orders barring diversity, equity and inclusion programs at all educational institutions that receive federal funds.

A warning issued Monday by Linda McMahon, the newly confirmed secretary of education, made clear that the administration had its sights set on Columbia. Ms. McMahon warned that Columbia would face the loss of federal funding, the lifeblood of major research universities, if it did not take additional action to combat antisemitism on campus.

Dr. Armstrong, the interim president, said Columbia was going through a “time of great risk to our university” and that the cutoff of government funds would be felt in “nearly every corner” of the school.

“There is no question that the cancellation of these funds will immediately impact research and other critical functions of the University, impacting students, faculty, staff, research, and patient care,” Dr. Armstrong wrote.

A statement issued by four federal agencies on Friday announcing the funding cuts referred to ongoing protests and antisemitic harassment at Columbia, though to what extent pro-Palestinian demonstrations on campus can be considered antisemitic remains in dispute.

Issued by the departments of Justice, Education and Health and Human Services, along with the General Services Administration, the statement did not indicate what grants would be terminated. But it said that the Health and Human Services and Education Departments would soon issue stop-work orders to immediately freeze the university’s access to some funds.

The statement said that the cancellations represented the “first round of action” and that additional cancellations were expected to follow.

More than a quarter of Columbia’s $6.6 billion in annual operating revenue comes from federal sources, according to its 2024 financial statements.

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.

Because grants span multiple years, Columbia holds more than $5 billion in federal grant commitments, according to the federal government. While the university’s large endowment can help to plug funding gaps, it is not clear if the school will use it for that purpose. The endowment was almost $15 billion at the end of the last academic year, according to figures published by the school.

The school also faces three federal investigations into allegations of antisemitism on campus that have been announced over the past several weeks. In her email on Friday, Dr. Armstrong said Columbia would “continue to take serious action toward combating antisemitism on our campus.”

Ms. McMahon said in her statement on Friday that “universities must comply with all federal anti-discrimination laws if they are going to receive federal funding.”

“For too long, Columbia has abandoned that obligation to Jewish students studying on its campus,” she said.

Ms. McMahon met with Columbia’s interim president on Friday and posted on social media about an hour after the funding cuts went public that the meeting had been “productive.”

“Look forward to working together to protect all students on their campus,” Ms. McMahon wrote.

A Columbia spokeswoman said the university was reviewing the Trump administration’s announcement and that it pledged to work with the federal government to restore the funding.

Columbia’s campus in the Morningside Heights neighborhood of Manhattan became a hotbed of protest last year, when students established a camp on the college lawn to oppose the war in Gaza and express support for Palestinian rights.

But the protests at Columbia also drew allegations of antisemitism, after some Jewish students said they had experienced harassment on campus. Others complained of offensive signs or chants at protests, including some that appeared to downplay the severity of the Hamas-led terrorist attack against Israel on Oct. 7, 2023, or to directly support it.

During the attack, Hamas and its allies killed about 1,200 people and took about 250 hostages, some of whom remain in Gaza, according to the Israeli authorities. Israel’s subsequent war in Gaza has killed tens of thousands of people, according to health officials in Gaza, and has displaced almost two million more and destroyed most of the territory’s infrastructure and economy.

To end the encampment, Columbia’s administration requested assistance from the New York Police Department, whose officers swept through the protest area in riot gear and arrested 109 people, mostly students. The police were called again to intervene after protests escalated and demonstrators took over Hamilton Hall, a campus building.

The decision to call in the police drew criticism from within higher education, with many faculty members and administrators recoiling from footage in the news media of riot police arresting students. The move also heightened pressure on Columbia’s president, Minouche Shafik, who resigned in August after a brief and tumultuous tenure largely defined by the protest crisis.

But the steps Columbia took last year, including the decision to call in the police, did not mollify the concerns of congressional Republicans. They continued to accuse Columbia and other universities of failing to adequately address allegations of antisemitism, even though a subset of the pro-Palestinian protesters are Jewish themselves.

While the outpouring of student support for the pro-Palestinian demonstrators lessened this fall, sporadic protests continued. The main protest group on campus became more vocally supportive of armed resistance against Israel, leading some Jews on campus to demand that further action be taken.

But efforts to discipline students for pro-Palestinian activism also set off a backlash. Students at Barnard, Columbia’s affiliated women’s college, held two sit-ins during the past week to call for the reinstatement of two students who had been expelled for disrupting a “History of Modern Israel” class and handing out fliers with slogans such as “Crush Zionism.”

Students and faculty members on campus on Friday expressed anger at the federal funding cut, even as some acknowledged that antisemitism was a concern.

Ilana Cohen, a Jewish woman and recent Barnard graduate, said she wanted to see progress made to combat antisemitism, but was skeptical that the funding cut would promote that goal.

“I find it hard to believe that they’re acting out of care for Jewish students,” she said. “In the past year, I have felt that Jewish voices on this campus have been treated like a pawn in a political game.”

Joseph Howley, a classics professor at Columbia who has been supportive of the students’ First Amendment right to protest, blasted the cuts and said that he believed they were unlawful.

“My only question right now is whether the university will be taking Trump to court over this or just rolling over and accepting it,” he said.

Radhika Sainath, a senior staff attorney at Palestine Legal, which is representing Palestinian students in a civil rights case against Columbia, called the government move “a bullying attempt on a massive scale” that was meant to punish Columbia and its students for their exercise of free speech.

She said it was it was “really important in this moment that we’re in that Columbia University — and the many other universities that will soon be in Columbia’s boat — not bow to this McCarythite attempt to stop any and all criticism of Israel.”

But others said the move was justified, even if they hoped funding cuts would be short lived.

“Columbia has an antisemitism crisis, and for months, I have worked with faculty, staff, students, parents and alumni to urge the administration to act quickly to address this crisis and avoid lasting damage to the university,” Brian Cohen, the executive director of Hillel on campus, said in a statement.

“I hope this federal action is a wake-up call to Columbia’s administration and trustees to take antisemitism and the harassment of Jewish students and faculty seriously,” Mr. Cohen continued, “so that these grants can be restored, the vital work of the university can continue and that Columbia can become, once again, a place where the Jewish community thrives.”

Anvee Bhutani contributed reporting.