Columbia University agreed on Friday to overhaul its protest policies, security practices and Middle Eastern studies department in a remarkable concession to the Trump administration, which has refused to consider restoring $400 million in federal funds without major changes.

The agreement, which stunned and dismayed many members of the faculty, could signal a new stage in the administration’s escalating clash with elite colleges and universities. Harvard, Stanford, the University of Michigan and dozens of other schools face federal inquiries and fear similar penalties, and college administrators have said Columbia’s response to the White House’s demands may set a dangerous precedent.

This week, the University of Pennsylvania was also explicitly targeted by the Trump administration, which said it would cancel $175 million in federal funding, at least partly because the university had let a transgender woman participate on a women’s swim team.

Columbia, facing the loss of government grants and contracts over what the administration said was a systemic failure to protect students and faculty members “from antisemitic violence and harassment,” opted to yield to many of the administration’s most substantial demands.

The university said it had agreed to hire a new internal security force of 36 “special officers” who will be empowered to remove people from campus or arrest them. The wearing of face masks on campus will also be banned for the purpose of concealing identity during disruptions, with exceptions for religious and health reasons.

Columbia will also adopt a formal definition of antisemitism, something many universities have shied away from even as they, like Columbia, faced pressure to do so amid protests on their campuses over the war in Gaza. Under the working definition, antisemitism could include “targeting Jews or Israelis for violence or celebrating violence against them” or “certain double standards applied to Israel,” among other issues.

Taken together, the administration’s plan — issued in an unsigned, four-page letter — reflected a stunning level of deference to the Trump administration from a top private research university.

Columbia’s interim president, Katrina A. Armstrong, said in a separate letter that the university’s actions were part of its effort to “make every student, faculty and staff member safe and welcome on our campus.”

“The way Columbia and Columbians have been portrayed is hard to reckon with,” Dr. Armstrong said. “We have challenges, yes, but they do not define us.”

She added: “At all times, we are guided by our values, putting academic freedom, free expression, open inquiry, and respect for all at the fore of every decision we make.”

The Trump administration demanded each of the changes in a letter to Columbia officials on March 13. It was not immediately clear whether the university’s actions would be sufficient to reclaim the $400 million in federal money. A spokeswoman for the Education Department, one of three federal agencies named in the letter, did not immediately respond on Friday to a request for comment, including to questions about the potential restoration of federal funding.

In perhaps the most contentious move, Columbia said it would appoint a senior vice provost to oversee the Middle Eastern, South Asian and African Studies Department. The White House had demanded that the department be placed under academic receivership, a rare federal intervention in an internal process that is typically reserved as a last resort in response to extended periods of dysfunction.

Columbia did not refer to the move related to the Middle Eastern studies department as receivership, but several faculty members said that it appeared to resemble that measure.

Legal scholars and advocates for academic freedom expressed alarm on Friday over what they described as Columbia’s dangerous surrender to President Trump at a perilous moment for higher education. Some critics of the university’s response said they feared the White House could target any recipient of federal funds, including K-12 public schools, hospitals, nursing homes and business initiatives.

Sheldon Pollock, a retired former chair of the university’s Middle Eastern studies department, said in a text message that “Columbia faculty are utterly shocked and profoundly disappointed by the trustees’ capitulation to the extortionate behavior of the federal government.”

“This is a shameful day in the history of Columbia,” Dr. Pollock said, adding that it would “endanger academic freedom, faculty governance and the excellence of the American university system.”

The moves by Columbia were first reported by The Wall Street Journal.

The school’s response to the administration’s demands was the latest turn in a turbulent phase that began 17 months ago, when pro-Israel and pro-Palestinian students organized competing protests in the days after the Hamas-led Oct. 7, 2023, attack on Israel.

Since then, the Manhattan campus has experienced a rare summoning of the police to quell protests, the president’s resignation and the detention of Mahmoud Khalil, a recent graduate, by federal immigration officials.

The extraordinary cancellation of funding for the university escalated the crisis, imperiling research that includes dozens of medical and scientific studies. (The university did not mention the loss of funds in outlining the steps it was taking.)

On social media, Jameel Jaffer, the director of the Knight First Amendment Institute at Columbia, called it “a sad day for Columbia and for our democracy.”

Others said that a wholesale overhaul was appropriate in light of the conflict and tension on campus in recent semesters.

Ester R. Fuchs, who co-chairs the university’s antisemitism task force, said that many of the administration’s changes appeared to be issues that the group had previously highlighted.

“What’s fascinating to me is a lot of these are things we needed to get done and were getting done, but now we’ve gotten done more quickly,” said Dr. Fuchs, who is also a professor of international and public affairs and political science.

She added: “We are completely supportive of principles of academic freedom.”

Among other changes, the university also said that the administration would work to adopt a universitywide “position of institutional neutrality.” It said that it would move an independent panel of faculty, students and staff members who handle disciplinary procedures under the provost’s office — and that members would be “restricted to faculty and administrators only.”

The school also agreed to review its admissions policies for potential bias after it “identified a recent downturn in both Jewish and African American enrollment,” and last week announced a range of disciplinary actions against an undisclosed number of students.

Despite the overhaul, the current fraught chapter in Columbia’s 270-year history may not be over. The Trump administration has told the university that meeting its demands was “a precondition for formal negotiations” over a continued financial relationship and that the White House may call for other “immediate and long-term structural reforms.”

Columbia’s changes are notable for their scope and for how quickly they were made. But it is not the only institution to make concessions as the White House indicates that its campaign against elite universities and colleges will not end at the Morningside Heights campus.

Federal money is the lifeblood of major research universities, and some have begun to keep quiet on hot-button issues in hopes of escaping the administration’s ire. Many, including the University of California this week, have retreated from diversity-related efforts.

Many of the changes Columbia agreed to make involve issues that have been points of contention on campus for some time.

Face masks, for example, emerged as a source of conflict last year amid the Gaza protests, with demonstrators saying they should be able to conceal their identities to avoid being doxxed, and others arguing that mask-wearing makes it harder to hold protesters accountable if their actions veer into harassment.

The detainment this month of Mr. Khalil, a prominent figure in the protests who stood out because he chose not to wear a mask, cast a spotlight on the issue.

But putting the Middle Eastern studies department, which has long been in a pitched battle over its scholarship and the employment of professors who describe themselves as anti-Zionist, under outside scrutiny provoked unique outrage.

Columbia said that the senior vice provost would review curriculum and hiring in several programs, including the Center for Palestine Studies and the Institute for Israel and Jewish Studies. The university said the move was aimed at “promoting excellence in regional studies.”

But Michael Thaddeus, a Columbia math professor who described reading Dr. Armstrong’s letter with “profound disappointment and alarm,” called it “a giant step down a very dangerous road.”

He worried that the Middle Eastern studies department would effectively be run by “a member of Columbia’s thought police” who could interfere with anything from course offerings to faculty appointments. “It strikes at the heart of academic freedom,” Professor Thaddeus said.

“Of all the bad things,” he continued, “this one is really the worst.”

Katherine Rosman contributed reporting.

The Trump administration moved early Friday to detain an international student at Cornell University who has led protests on its Ithaca, N.Y., campus, in what appeared to be the latest effort to kick pro-Palestinian activists out of the United States.

A lawyer for Momodou Taal, a doctoral student in Africana studies, said in court papers that he had been notified by email early Friday morning that U.S. Immigration and Customs Enforcement was seeking Mr. Taal’s surrender.

Last year, Mr. Taal was among a group of pro-Palestinian activists who shut down a career fair on the Cornell campus that featured weapons manufacturers. As a result, the university had ordered him to study remotely for the spring semester.

Mr. Taal, a great-grandson of Gambia’s first president, Sir Dawda Kairaba Jawara, is a citizen of both Gambia and the United Kingdom. According to court documents, Mr. Taal, who is here on a visa, said he feared deportation in part because his name had been circulated on social media and in media reports as a potential ICE target.

The move to detain Mr. Taal comes as the Trump administration tries to deport other pro-Palestinian students and academics.

About two weeks ago, Mahmoud Khalil, a permanent U.S. resident of Palestinian descent who recently obtained a master’s degree from Columbia University, was detained in New York. On Monday, the government detained Badar Kahn Suri, an Indian citizen who was studying and teaching at Georgetown University, claiming he had violated terms of his academic visa. Other students have also been targeted.

ICE did not immediately return a request for comment.

Last weekend, Mr. Taal filed a pre-emptive lawsuit to block possible action against him. A hearing had been scheduled in that case for Tuesday in Syracuse, N.Y. A lawyer for Mr. Taal, Eric T. Lee, argued in the lawsuit that his client was exercising his right to free speech and that there were no legitimate grounds for his deportation.

The lawsuit also challenged the legality of Mr. Trump’s executive order to “combat antisemitism” that instructed federal agencies to deport immigrants whose actions could be regarded as “antisemitic or supportive of terrorism.”

Earlier this week, neighbors saw law enforcement agents near Mr. Taal’s apartment building by Cornell’s campus, according to affidavits filed in the lawsuit in the Northern District of New York.

“This does not happen in a democracy. We are outraged, and every American should be too,” Mr. Lee said in a statement.

Lawyers for Mr. Taal are asking the court to delay his surrender to ICE, pending the outcome of the litigation. On Thursday, hundreds of Cornell students and supporters held a rally in support of Mr. Taal, who is also the host of a podcast called “The Malcolm Effect.”

In October 2023, three days before Hamas fighters attacked Israel, Columbia University’s new president stood outside Low Library and posed a foundational question.

“What,” she asked, “does the world need from a great university in the 21st century?”

The president, Nemat Shafik, argued that the world required much. Rigorous thinkers who were grounded in the age’s great debates. Researchers whose breakthroughs could transform societies. Universities that extended their missions far beyond their gates.

Seventeen months later, Dr. Shafik is gone and the Trump administration is offering a far different answer. The ideal Dr. Shafik described, much of it historically bankrolled by American taxpayers, is under siege, as President Trump ties public money to his government’s vision for higher education.

That vision is a narrower one. Teach what you must, defend “the American tradition and Western civilization,” prepare people for the work force, and limit protests and research.

“I have not experienced, across 46 years of higher education, a period where there’s been this much distance” between the agendas of university leaders and Washington, said Robert J. Jones, the chancellor of the University of Illinois Urbana-Champaign.

The outcome of this clash over the purpose of higher education stands to shape American culture for a generation or more. If the president realizes his ambitions, many American universities — public and private, in conservative states and liberal ones — could be hollowed out, imperiling the backbone of the nation’s research endeavors.

Two months into Mr. Trump’s term, universities are laying off workers, imposing hiring freezes, shutting down laboratories and facing federal investigations. After the administration sent Columbia a list of demands and canceled $400 million in grants and contracts, university leaders across the country fear how the government might wield its financial might to influence curriculums, staffing and admissions.

“Colleges have gotten hundreds of billions of dollars from hard-working taxpayers,” Mr. Trump said in a campaign video. “And now we are going to get this anti-American insanity out of our institutions once and for all. We are going to have real education in America.” The goal, Mr. Trump declared, is to reclaim “our once-great educational institutions from the radical left.”

Other Republicans have spoken, often in more measured language, about their own frustrations with higher education. Senator Bill Cassidy, the Louisiana Republican who chairs the Senate Committee on Health, Education, Labor and Pensions, bluntly complained during a hearing last month that colleges were “not preparing students to succeed in the modern work force.”

With presidential power magnified by a largely genuflecting Congress, Mr. Trump’s challenges to academic freedom and First Amendment protections have not provoked broad and visible public outrage. The sobering reality for university leaders is that Mr. Trump has the administrative upper hand, and academia has startlingly few vocal allies.

The fusillade against higher education led by Mr. Trump and Vice President JD Vance — men with Ivy League degrees — is more furious than past conservative crusades against the country’s elite academic institutions. The administration, though, is capitalizing on imperfections that have been tearing at the system’s stature for years.

“His genius was in understanding and then exploiting the resentments, the anxieties, and the vulnerabilities of” voters who already had “critical sentiments” toward higher education, Ronald J. Daniels, the president of Johns Hopkins University, wrote of Mr. Trump in his 2021 book, “What Universities Owe Democracy.”

Private polling conducted for universities shows that many people believe that these nonprofit institutions are anything but — one consequence of high tuition costs. Even though a college education almost always provides graduates with higher lifetime incomes, rising debt has made the value of a degree a matter of debate. Politicians have eagerly caricatured colleges as sanctuaries of intolerance and “wokeism” where admissions processes have sometimes considered race or favored the well-connected.

For all of their grand talk — “For Humanity” is the name of Yale University’s $7 billion fund-raising campaign — administrators and professors often acknowledge that they have not mustered easy-to-digest responses against even routine criticisms.

Universities strained to be more accessible, building up more diverse classes and handing out more financial aid. But Chancellor Jones, who will become the University of Washington’s president this summer, nevertheless described higher education’s public relations strategy as “a work in progress.”

Many leaders concede that while the role of the university in American life is clear to them, it has grown muddled to many.

“Higher education has always been able to stand up and invoke its moral authority,” said Roger L. Geiger, a distinguished professor emeritus at Pennsylvania State University and a leading authority on the history of American colleges. “What’s happened is they’ve simply lost that moral authority.”

The Pew Research Center found in 2012 that 26 percent of Americans believed that colleges and universities were negatively affecting the United States. Last year, even before the campus demonstrations that led to thousands of arrests, Pew reported that figure had increased to 45 percent.

Much of Mr. Trump’s higher education agenda during his first term empowered for-profit colleges. Now, though, Mr. Trump is taking clearer aim at the cultures and missions of major nonprofit universities. His tactics, university officials and researchers believe, could throw American higher education toward an earlier time — closer to when, as Dr. Shafik put it, universities “were kept separate from the world around them.”

American higher education predates the republic itself. Harvard, for example, was established in the colonial period to educate clergymen. George Washington’s idea for a national university was never realized, but Abraham Lincoln found more success pursuing the idea that higher education was entwined with American ambition when he signed the measure that led to publicly funded land-grant institutions.

Research became a focus of universities late in the 19th century. The nation’s reliance on universities greatly accelerated during and after World War II, as the United States began to lean on academia more than most other countries.

Essential to the system was Washington’s new willingness to underwrite overhead costs of expensive research projects. By 1995, the National Academy of Sciences concluded that universities were “the core strength” of the American research-and-development apparatus. Universities also assumed part of the United States’ soft-power strategy, working on foreign aid projects that spanned the globe.

That symbiotic arrangement is now in jeopardy. The administration has framed its proposed cuts to overhead expenses, for instance, as a way “to ensure that as many funds as possible go toward direct scientific research costs.” But administration officials have also depicted the longstanding framework in harsh terms, including the assertion that it created a “slush fund” for liberal university administrators.

As Dr. Geiger put it, the Trump administration’s approach represented “a new era.” Besides upending individual studies, cuts to federal money could unleash dramatic consequences for the structures and objectives of universities.

“No one can assume, for example, that biochemistry is going to have a sustained future of generous funding,” said John Thelin, a professor emeritus at the University of Kentucky and a former president of the Association for the Study of Higher Education.

He could think of no president, provost or medical school dean who had, in recent years, appeared particularly nervous about an evaporation of funding. These days, it is hard to find a president, provost or medical school dean who is not anxious about something.

At Illinois, the federally funded Soybean Innovation Lab will close next month. Dr. Jones fears that research on everything from insulin production to artificial intelligence could ultimately wither, undermining the university’s ability to advance what he called “the public good.”

“Before, we were just trying to tell our story to improve the value proposition in the eyes of the public, but now it becomes a bigger, much larger issue than that,” said Dr. Jones, one of the few top university chiefs who have been willing to be interviewed on the record since Mr. Trump’s inauguration.

The threat is also acute at private institutions, even those with the biggest war chests. Johns Hopkins said last week that it would eliminate more than 2,000 jobs in the United States and overseas, the largest round of layoffs in its history. The University of Pennsylvania, Mr. Trump’s alma mater, is among the universities with new hiring freezes. (It announced that step before the Trump administration said on Wednesday that it would pause about $175 million in funding for Penn because it had allowed a transgender woman to compete on its women’s swim team.)

In recent weeks, presidents at public and private universities alike have weighed how long any institutional lifelines could last. But professors doubt that a major university can meet its modern ambitions without a relatively open spigot of federal support.

“Ultimately, the university cannot exist without research,” said Brent R. Stockwell, the chair of biological sciences at Columbia. “It would be really, really more akin to a high school or a local community college where you’re just teaching some classes without world-class researchers bringing the frontier of knowledge into the classroom.”

So far, Mr. Trump has not signaled any interest in retreat. That has left academic leaders searching urgently for how to save an ideal they insist is imperative.

Asked whether he feared a wholesale remaking of the American university, Dr. Jones replied that he did not like to use the word “fear.” But, he added, “it is a concern — I can’t say that it is not one of those things that a lot of us are concerned about.”

Sharon Otterman contributed reporting.