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Since President Trump took office, colleges have faced civil rights investigations, dealt with vague guidance and directives banning race-based programming, and grappled with ruinous grant cuts—all of which has upended operations at institutions.

But while some of those attacks from the new administration were expected, one tactic has loomed largest, particularly for research universities dependent on federal grants and contracts—the indiscriminate suspension of billions in federal funds with little justification from the administration beyond accusations of failing to address antisemitism. So far, the federal government has put nearly $6 billion on hold at nine universities, though some have made concessions to get the money back.

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Jon Fansmith, the senior vice president for government relations and national engagement at the American Council on Education, said that it’s not just about the billions in funds at stake but more about what the money represents and funds—the research that drives higher education.

It’s about the ability of “the researchers who are running labs, the staff, aspiring students and others who are performing this incredibly valuable work to benefit everybody,” he said. “It’s a blunt-force, brutal effort that is really harmful.”

No administration, Fansmith added, has frozen funds like this.

“It’s the definition of arbitrarily picking political targets and using threats and freezes and other things to try to bend institutions,” he said. “This is yet entirely unprecedented.”

Columbia University was the first institution to see such a blanket suspension. In early March, a multiagency task force said it was freezing $400 million in grants and contracts at the university after it accused Columbia officials of failing to protect Jewish students. That move was roundly criticized, with experts, Columbia faculty and others describing the freeze as deeply alarming and arguing it was unlawful in part because the administration didn’t follow the required processes to pull funding. (Some supporters did praise the administration for sending a strong message.)

Undeterred, the administration pressed forward and quickly put funds on hold at several other universities, mostly in the Northeast. But most got news of the freezes from media reports and social media posts—not direct communication from the administration. For example, leaders at Northwestern University, where the government froze $790 million, didn’t hear anything official about the freeze for weeks after media outlets first reported on it.

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And aside from stripping a college of its tax-exempt status or of eligibility for federal student loans, cutting of federal funds is one of the most powerful levers that the administration can pull, Fansmith said. He quickly added that “these are not legal actions [Trump officials] are taking. They don’t have any statutory or regulatory authority to suspend research on the basis of accusations.”

Instead, Fansmith sees the freezes as a way “to force a negotiation so they can claim victory when they lack any sort of authority or any sort of evidence that would allow them to do it in the appropriate way.”

In some cases, the government froze the funds before making its demands, which have included universities making sweeping changes to their admissions, hiring and discipline practices. In other instances, like at Harvard University, the funds stopped flowing after the university rejected the demands. Harvard is so far the only university to fight a funding pause, arguing in a lawsuit filed in April that the government’s actions violate the First Amendment and amount to retaliation.

“All told, the tradeoff put to Harvard and other universities is clear: Allow the Government to micromanage your academic institution or jeopardize the institution’s ability to pursue medical breakthroughs, scientific discoveries, and innovative solutions,” the university’s lawyers wrote in the initial complaint.

A federal judge heard arguments in the case in July but has yet to rule.

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Fansmith said the judge’s ruling will “establish a lot of precedence about what the limits of executive authority are.” He maintains that Harvard has the law on its side and that there’s no way to defend the administration’s actions.

“We’ll see, but certainly we’re in a very ambiguous and uncertain space,” he said. “As those decisions pile up, as those precedents build, it will become easier to push back.”

The White House didn’t respond to a request for comment, but Trump officials have repeatedly defended the freezes as legal, arguing the federal government has broad power to impose certain conditions on grants and contracts.

“The federal government grants funds to universities through contracts that include explicit conditions requiring the agreements effectuate the policy purposes of the federal government,” lawyers for the government argued in a motion related to the Harvard case. “If they fail to meet these conditions, the grants are subject to cancellation. It is the policy of the United States under the Trump Administration not to fund institutions that fail to adequately address antisemitism in their programs.”

Three universities have cut deals to get their money back, and more agreements are expected, though the colleges aren’t openly discussing the negotiations. Columbia was the first to formally settle, and government officials called that deal—which included a $221 million payout—a template for other universities to follow. Brown University later agreed to similar terms and committed to spend $50 million over 10 years to support workforce development in Rhode Island.

At the same time, the administration is resuming the use of blanket freezes as a way to force changes at universities. In the last month, Duke University and the University of California, Los Angeles, saw millions in grants suspended.

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Duke University officials have said little publicly, but UCLA officials have condemned the administration’s decision to freeze its funding.

“This is not only a loss to the researchers who rely on critical grants,” UCLA chancellor Julio Frenk told the campus community. “It is a loss for Americans across the nation whose work, health, and future depend on the groundbreaking work we do.”

From UCLA, Trump is demanding $1 billion to settle the government’s claims. California governor Gavin Newsom called that move “extortion” and has pledged to sue.

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Nearly 80 percent of the $5.7 billion the administration has frozen since March remains on hold. Officials at Columbia and Brown have publicly said the government restored the money. But with the Trump administration working to significantly cut federal research dollars going out the door at all, the pain might not be entirely over for these institutions.

Meanwhile, more universities could find themselves facing similar freezes. In August, administration officials accused George Washington University and George Mason University of violating Title VI of the Civil Rights Act of 1964, which bars discrimination based on race and national origin. In George Mason’s case, the Education Department demanded that the university president personally apologize—a request the leader rejected this week.

Although only a few institutions have been affected, Fansmith said other college presidents should be concerned that they could face a similar penalty. Supporting a transgender student or having policies that the administration disagrees with could trigger a freeze, he added.

“What [Trump officials] have shown is they will not follow the rules and the laws in a way that gives you some sense of what compliance actually looks like, because it’s irrelevant,” he said.

Jessica Blake contributed to this report.