It was an obscure, 44-word demand toward the end of the Trump administration’s ultimatum to Columbia University this month ordering a dramatic overhaul of admissions and disciplinary rules. But it could prove to have consequences for colleges and universities nationwide.

With $400 million in canceled government grants and contracts on the line, federal officials ordered Columbia’s administration to place the university’s Middle Eastern studies department under academic receivership for at least five years.

Typically, a receivership is handled internally. University administrators can take the rare step of imposing the measure when a department descends into chaos. It is viewed as a last-resort solution to extended periods of internal strife and dysfunction.

This time is different. The call for a receivership is coming from outside the university — and directly from the White House. And it arrives at a moment when dozens of other colleges and universities are facing federal inquiries and fear a fate similar to Columbia’s.

“It is one small department in one university,” said Sheldon Pollock, a retired former chair of the Middle Eastern studies department at Columbia. “But it will reverberate across the entire country.”

The interdisciplinary program at the center of the government’s demand — the Middle Eastern, South Asian and African Studies Department — has been in a pitched battle for decades over its scholarship and employment of faculty members who describe themselves as anti-Zionist.

Several historians and veteran professors said that the move by the federal government to intervene in an academic department at a private university would be unparalleled in the modern history of U.S. higher education.

Laurie A. Brand, a professor emerita at the University of Southern California, who described the department as one of the most respected in the field, compared the move to the Turkish government’s centralized control of higher education during its “hard authoritarian turn” in the 2010s.

“I certainly don’t remember a case in the United States,” said Dr. Brand, the chair of the Committee on Academic Freedom at the Middle East Studies Association, an organization of scholars who focus on the region.

The swirling questions about the department’s future have emerged as the latest crisis for Columbia, where pro-Palestinian demonstrations against the war in Gaza ignited a national protest movement and animated debate over free speech and antisemitism. The federal government accused the university last week of failing to safeguard students and faculty members “from antisemitic violence and harassment,” calling for changes that include the school formalizing its definition of antisemitism.

The government said that it had extended its deadline to the end of Friday for Columbia to respond to its ultimatum, which would include offering a timeline for placing the Middle Eastern studies department under receivership.

College administrators across the nation are closely watching whether Columbia acts with deference or defiance.

As higher education institutions face federal scrutiny, many see the dispute over the department as a high-stakes test case for other Middle Eastern studies programs — and for other endeavors that could run afoul of conservative orthodoxy, such as centers for the study of climate change or gender and sexuality.

Dr. Pollock described the government’s “intrusion” as “jaw-dropping” and “a historic and astonishing event.”

Such a move would signal “the beginning of the end of the American university as we’ve known it since 1915,” the year that the American Association of University Professors first codified guidelines and practices for academic freedom.

A spokeswoman for the Department of Education, one of three federal agencies named in the letter to Columbia, did not respond to questions about the rationale for the receivership.

In a letter to the university on Wednesday, Columbia’s interim president, Katrina A. Armstrong, seemed to acknowledge the growing concern over how the school might respond.

“Legitimate questions about our practices and progress can be asked, and we will answer them,” Dr. Armstrong wrote. “But we will never compromise our values of pedagogical independence, our commitment to academic freedom or our obligation to follow the law.”

President Trump has previously homed in on Middle Eastern studies programs for potential bias, including in his first term. The Education Department, under its former head, Betsy DeVos, ordered Duke University and the University of North Carolina at Chapel Hill to remake their jointly run Middle East studies program, accusing it of offering students a biased curriculum in violation of federal funding standards.

It was one example of the charged conflict over Middle Eastern studies, which has historically inspired debate, in part because the discipline can highlight academic scholarship that casts Israel in a negative light. At some institutions, students, professors, alumni and donors have been divided over the distinction between anti-Zionism and antisemitism in such work — and whether the two should be regarded as distinct issues.

Columbia’s Manhattan campus — and its roughly 50-member Middle Eastern, South Asian and African Studies Department — have been a hot spot for these disputes.

The department was a central focus of a 2004 documentary called “Columbia Unbecoming,” which interviewed students who had taken classes in the department and described facing intimidation from faculty members for their pro-Israel views. Its central thesis, which has been strenuously debated, depicted a systemic silencing of Jewish students in campus culture.

During the past 17 months of fighting in Gaza, the department has come under a wave of renewed scrutiny, including during a high-profile hearing on antisemitism last spring.

A number of Congressional Republicans took issue with some faculty members, including Joseph Massad, a tenured professor of Palestinian Christian descent who teaches modern Arab politics and intellectual history. Many students and alumni were enraged over an article he wrote after the Hamas attack, which included descriptors like “resistance offensive” and “awesome.”

Michelle Steel, a former Republican representative from California, said during the hearing that the article illustrated that the department had been “extremely hostile to both Israel and Jewish students” for more than two decades, and asked whether the school would consider “placing the department into receivership.”

Nemat Shafik, Columbia’s president at the time, avoided a direct answer. “Academic departments at Columbia are — there isn’t really a notion of receivership,” Dr. Shafik, who resigned from her post in August, responded.

Some Jewish organizations in recent months called on Columbia’s leadership to overhaul the department. Kenneth L. Marcus, the founder of the Brandeis Center in Washington, D.C., said that many Jewish students during the past two decades had “simply been warned to avoid the program altogether.”

It may be debatable whether academic receivership is the answer, Mr. Marcus said. Still, he called it a milestone for federal officials to recognize “that the campus problem cannot be solved without a faculty solution.”

The chair of the Columbia department, Gil Hochberg, did not respond to requests for comment.

It remains unclear what an academic receivership might entail. Several advocates of academic freedom raised concerns in interviews that the government might seek to influence the selection of a new department chair, who could have broad leeway to reshape course content or pursue the dismissal of tenured faculty members.

Others worried that the move could set a precedent for the Trump administration to make threats to federal funding at other universities over scholarship that it finds unfavorable. One professor wondered whether history departments could come under fire for courses that federal officials believed portray slavery and segregation too negatively.

Radhika Sainath, a senior staff attorney at Palestine Legal, which is representing Palestinian students in a civil rights case against Columbia, said that Middle Eastern studies departments had often been targeted for punishment or defunding because they challenged dominant narratives about Israel.

Ms. Sainath called the receivership demand “straight out of an authoritarian playbook where attacking universities is the first step,” and “any institution that represents opposition to Trump’s agenda” could be next.

It would not be Columbia’s first experiment with academic receivership. Some two decades ago, school administrators placed the Middle Eastern studies department under a one-year receivership and appointed an interim chair in part because of struggles to find a new leader, Dr. Pollock, the former chair, said.

And amid internal disputes over cultural shifts in the study of literature, Columbia leaders appointed a scholar from a Pennsylvania university to lead the English department in the early 2000s. A weekly newspaper in New York described the stakes in now familiar terms: “Crisis at Columbia.”

David Damrosch, a Harvard professor of comparative literature who was a member of Columbia’s English department at the time, said the move helped mend divisions. But he added that a receivership “might be the single most dangerous thing the administration has demanded out of everything.”

To Dr. Damrosch, who has studied academic culture at colleges, the current turmoil was vaguely reminiscent of a 1940s episode at the school now known as Iowa State University.

The school’s economics department — in a paper on economic policy for wartime food production — had proposed replacing butter with margarine, said Dr. Damrosch. The dairy industry and its supporters in the state legislature “went ballistic,” he said, pressuring the school’s president to place the department under receivership.

The move triggered an immediate backlash and mass departure of faculty members.

It might have also played a small role in the reshaping of the higher education landscape: At least six professors fled to Chicago, where they helped build one of the most renowned economics departments in the world.