The Trump administration’s move this week to choke off Harvard University’s access to future federal funding came after a scathing letter from the college accusing the administration of distorting evidence to show that the school violated civil rights laws by allowing antisemitism to persist on campus.
The brewing feud represents an escalation of tensions between Harvard and the administration, which just weeks ago seemed on the verge of agreeing on a deal to keep federal funds flowing to the university.
In a strongly worded, 163-page letter with attachments on Sept. 19, which has not been previously reported, Harvard assailed the government’s findings. The university accused investigators at the Health and Human Services Department of relying on “inaccurate and incomplete facts,” failing to meet a single legal requirement to prove discrimination and drawing sweeping conclusions from a survey of one-half of 1 percent of the student body.
Harvard painted a picture of a chaotic Trump administration rushing to leverage federal power against the university. For instance, it noted that the health department had chided the college for failing to produce certain records. But Harvard’s documents showed that the records in question had been provided in response to a request from the Education Department. Harvard said the health department never asked for those records.
Harvard said the health department’s decision to refer its findings to the Justice Department was “based on a fabricated and distorted interpretation of the record.”
The stark language was a departure from months of mostly measured tones from Harvard as the university has resisted the administration’s pressure campaign to impose President Trump’s political agenda on the nation’s elite colleges.
Mr. Trump and his administration have sought to exert control over who universities can hire, which students they should admit and what subjects should be taught by leveraging huge sums of federal research money. Those moves, which Harvard has maintained violate the college’s First Amendment rights and infringe on the nation’s long-held ideals of academic freedom, are aimed at shifting the ideological tilt of the higher education system, which the administration sees as hostile to conservatives and intent on perpetuating liberalism.
The administration’s reply to Harvard’s letter came on Monday, when the health department initiated a process to cut off Harvard from future federal research funding, which has increasingly become the lifeblood for the nation’s largest private and public colleges. In 2022, the health department accounted for nearly 81 percent of $41.6 billion in federal funding for research into agricultural science, environmental science, public health and other life sciences, according to government records.
Blocking Harvard from this funding would strike at a pillar of the university’s financial stability. Federal research dollars accounted for 11 percent of the college’s operating budget in 2024, with most of that funding authorized by the health department and the National Institutes of Health, an arm of the department that has long been one of the world’s largest public sources of biomedical research funding.
White House and health department spokesmen did not immediately respond to a request for comment.
Harvard officials have been anxious about the long-term implications of losing federal funding. Dr. Alan Garber, the university’s president, and other campus leaders have privately wrestled with how to defend the college’s First Amendment rights and restore billions of dollars of existing grants — while trying to avoid a larger, potentially untenable crisis of losing access to new research funding.
That tension helps explain the university’s response earlier this month, when Harvard lawyers lashed out, accusing the administration of ignoring facts that would undercut the health department’s findings.
According to documents reviewed by The New York Times, Harvard submitted reports, emails and other records to the administration this month showing that the health department’s findings cited incidents that occurred off campus and disregarded actions taken by Harvard during the past 18 months to fire employees and suspend students involved in harassment of Jewish men and women.
The only specific incident in the health department’s report that would show antisemitism disrupted a student’s access to education, Harvard lawyers wrote, was not a firsthand account.
“It is an anonymous account from one student,” according to Harvard’s letter. This student had said that “other students stopped going to a class because those other students did not feel safe.”
That example did not come from the health department’s independent investigation, according to the Harvard letter. It came from Harvard’s own internal investigation of antisemitism.
Another example of antisemitism cited by the health department was of a Jewish student who reported that her mezuza had gone missing. But Harvard noted that the decorative symbol of Jewish faith had been found by the university police in the hallway, three doors down from the student’s room. That suggested the mezuza “may have fallen because the adhesive tape used to affix it to the doorway had given way, and not because it was deliberately vandalized.”
The student who lost the mezuza, Sarah F. Silverman, later wrote a column for U.S. News & World Report saying her experience “should not be used as justification for destroying the university.” She wrote that she had never been contacted by government investigators — or anyone else from the administration — to discuss the incident.
For much of the past year, Harvard officials have publicly expressed regret over failing to respond more fully to complaints of antisemitism on campus. On Jan. 19, 2024, Dr. Garber announced the formation of the Presidential Task Force on Combating Antisemitism and Anti-Israeli Bias, saying that “reports of antisemitic and Islamophobic acts on our campus have grown, and the sense of belonging among these groups has been undermined.”
“We need to understand why and how that is happening — and what more we might do to prevent it,” Dr. Garber said at the time.
Still, imperfection is not illegal, Harvard told the health department this month, and civil rights laws require a significant burden of proof to be placed on the accuser. Congress devised civil rights laws this way, in part, to reduce the likelihood that the consequential statutes would be used as a political cudgel.
Part of the proof required by federal law includes demonstrating that the school actively ignored accusations of discrimination.
Harvard has argued that the university has “demonstrated swift, decisive action” to confront problems starting more than a year before the health department opened its investigation in February.
The university has put in place many of the recommendations from Dr. Garber’s task force and adopted and enforced new policies on campus protests. Harvard has also started other new initiatives that campus leaders described as promoting safety, accountability and civil discourse.
Judge Allison D. Burroughs of the Federal District Court in Boston has rebuked the administration for ignoring these gestures. On Sept. 3, she cited its repeated refusal to acknowledge the university’s concrete steps while ruling that the government broke the law by freezing billions in funding for Harvard.
The health department’s investigation relied largely on the university task force’s report that detailed anecdotes of reported antisemitism.
The health department referred its findings to the Justice Department, which has not taken any public action on the report.
Michael C. Bender is a Times correspondent in Washington.
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