BOSTON — A federal judge in Boston on Wednesday ordered the Trump administration to reverse its cuts of more than $2.6 billion in research funding for Harvard University, delivering a significant victory to the Ivy League school in its battle with the White House.

U.S. District Judge Allison Burroughs ruled the cuts amounted to illegal retaliation for Harvard’s rejection of the Trump administration’s demands for changes to Harvard’s governance and policies.

The government had tied the funding freezes to Harvard’s delays in dealing with antisemitism, but the judge said the university’s federally backed research had little connection to discrimination against Jews. “A review of the administrative record makes it difficult to conclude anything other than that (the government) used antisemitism as a smokescreen for a targeted, ideologically-motivated assault on this country’s premier universities,” Burroughs wrote. The country must fight antisemitism, she wrote, but it also must protect the right to free speech.

The ruling reverses a series of funding freezes that later became outright cuts as the Trump administration escalated its fight with the nation’s wealthiest university. The administration also has sought to prevent the school from hosting foreign students and threatened to revoke its tax-exempt status in a clash watched widely across higher education.

The restoration of federal money would revive Harvard’s sprawling research operation and hundreds of projects that sustained cuts. But whether Harvard actually receives the federal money remains to be seen. The government plans an immediate appeal, White House spokeswoman Liz Huston said in a statement, calling Burroughs an “activist Obama-appointed judge.”

“To any fair-minded observer, it is clear that Harvard University failed to protect their students from harassment and allowed discrimination to plague their campus for years,” Huston said. “Harvard does not have a constitutional right to taxpayer dollars.”

Harvard’s research scientists said they had been watching the case closely, but feared their funding would not be restored anytime soon.

“Many of us are worried that the federal government is going to appeal this decision or find other ways to obstruct the delivery of research dollars, despite the judge’s clear statement that the funding terminations were illegal,” said Rita Hamad, director of a center that researches the impact of social policies on health.

Beyond the courthouse, the Trump administration and Harvard officials have been discussing a potential agreement that would end investigations and allow the university to regain access to federal funding. President Donald Trump has said he wants Harvard to pay no less than $500 million, but no deal has materialized, even as the administration has struck agreements with Columbia and Brown.

Wednesday’s federal court ruling should embolden Harvard’s administration, said historian Kirsten Weld, president of Harvard’s chapter of the American Association of University Professors, which also prevailed in a lawsuit over the funding cuts. “We hope this decision makes clear to Harvard’s administration that bargaining the Harvard community’s rights away in a compromise with the government is unacceptable,” Weld said.

Harvard’s lawsuit accused the Trump administration of waging a retaliation campaign against the university after it rejected a series of demands in an April 11 letter from a federal antisemitism task force.

The letter demanded sweeping changes related to campus protests, academics and admissions. It was meant to address government accusations that the university had become a hotbed of liberalism and tolerated anti-Jewish harassment on campus.

Harvard President Alan Garber pledged to fight antisemitism. But, he said, no government “should dictate what private universities can teach, whom they can admit and hire, and which areas of study and inquiry they can pursue.”