The letter landed like a thud on Saturday in the inbox of Harvard University’s president, Alan M. Garber.
The message, from Linda McMahon, President Trump’s education secretary, conveyed an understanding of an emerging deal between Harvard and the White House that flew in the face of the terms the university had been insisting on.
Dr. Garber felt he had made clear in recent negotiations that the university would not agree to pay the federal government to settle a monthslong battle with the Trump administration over antisemitism on campus and other matters.
But Ms. McMahon’s Saturday message said the opposite. In it, she thanked Dr. Garber for what she portrayed as his commitment to sending $200 million to the government as part of a deal.
Dr. Garber wrote back to clarify Harvard’s position. But, in response, the administration doubled down, introducing terms that were so far-reaching that university officials saw them as nonstarters.
It was unclear whether Ms. McMahon’s interpretation of Harvard’s proposal resulted from a miscommunication or from a deliberate effort to force the university into a year-end deal after months of faltering negotiations.
Whatever the case, it was the latest twist in the long-running dispute between Harvard and the Trump administration, which has shaped up to be the marquee battle in the administration’s effort to exert more influence over elite colleges and universities it views as too liberal.
The episode also underscored the emerging role played by people inside the administration who want to extract more concessions from Harvard. And it raised new questions about whether some of those voices were more interested in preserving the power of the government’s threat against Harvard as a message to other universities than in reaching a settlement with the nation’s wealthiest university.
While the interactions between Dr. Garber and Ms. McMahon plunged the sensitive talks into deeper turmoil, they also highlighted the unpredictability of the Trump administration. They showed how even high-stakes negotiations that could shape the direction of the country were defined by inconsistencies, confusion, communication breakdowns and combativeness.
This account of the negotiations between Harvard and the Trump administration is based on interviews with three people with direct knowledge of the talksand a New York Times review of some correspondence between the government and the university.
Harvard declined to comment. A White House spokeswoman declined to comment, and the Department of Education did not respond to requests for comment.
The rupture in recent days stands out amid the twists and turns that started when the White House targeted Harvard because it saw it as an incubator of liberalism that violated the civil rights of white and Jewish people.
The university has acknowledged that antisemitism had spread through parts of Harvard, affecting to some extent hiring, coursework and the culture of the campus in Cambridge, Mass. Dr. Garber, who is Jewish, has said he was “sorry for the moments when we failed to meet the high expectations we rightfully set for our community,” and has taken steps to combat antisemitism at Harvard.
The Trump administration, though, has routinely depicted Harvard’s efforts as tardy and insufficient. And Mr. Trump has suggested that he is looking to punish Harvard for both perceived past misdeeds and its defiance this year.
The conflict blew open in April, when an administration lawyer mistakenly sent Harvard’s lawyers a batch of demands that included policies on admissions and hiring, and a push for Harvard to shut down any programs related to diversity, equity and inclusion.
Outraged by the demands, Harvard sued and received praise from students, faculty and alumni for standing up to Mr. Trump.
The university won a significant victory in that lawsuit in September — the Trump administration last week filed a notice of appeal — but it has also faced a blitz of federal investigations, a threat to disqualify it as a government contractor and an effort to block billions of dollars in federal research funding.
And although the university has an endowment of roughly $57 billion and nearly four centuries of history, Harvard officials concluded in the spring that it was probably untenable to overcome so many threats from Washington, especially since Mr. Trump was not scheduled to leave office until 2029.
It opened settlement talks, which proceeded in fits and starts. Mr. Trump publicly declared that a deal was imminent, writing online in June that it would “be ‘mindbogglingly’ HISTORIC, and very good for our Country.” By mid-August, Harvard and Trump officials alike were convinced that they had a framework for an agreement.
But personnel changes in the West Wing convulsed the talks, and Mr. Trump’s deputy chief of staff, Stephen Miller, has seemed to undermine proposed agreements with Harvard in private meetings, according to two administration officials involved in the discussions. A White House spokeswoman declined to comment on the claims.
Significantly, the Justice Department’s civil rights chief, Harmeet K. Dhillon, has gained increased influence over the talks, which she has argued have teetered too much in Harvard’s favor.
The White House initially broached the idea with Harvard over the summer of having it spend $500 million on work force training programs to resolve the dispute. But now the administration is insisting that $200 million of that sum be paid as a fine to the federal government.
Tensions over that demand helped shape the talks between Ms. McMahon and Dr. Garber, even as Harvard spent weeks awaiting feedback from the government on other possible adjustments to settlement language.
In her letter on Saturday, reviewed by The Times, Ms. McMahon said Harvard’s willingness to spend $300 million on technical and vocational education, “in addition to $200 million in cash,” was closely aligned with the administration’s ambitions for higher education.
She told Dr. Garber that administration lawyers had “returned edits” to a potential settlement, hoping, among other matters, to “clarify that Harvard will maintain specific policies to combat antisemitism and ensure Jewish students have equal educational opportunities on campus” and to “clarify how Harvard will certify ongoing compliance with the agreement.”
“Please reach out to me or my team with any questions — day or night,” Ms. McMahon wrote. “It is time to get this deal done.”
Dr. Garber’s response came hours later. He was, he wrote, “delighted to hear that you share the view that Harvard’s proposed investment in work force education programs holds immense promise for the nation.”
But the second paragraph of Dr. Garber’s letter included some pushback.
“I do need to clarify that, during our recent conversations, I described our work force investment proposal as one for $500 million — not for $300 million in addition to a $200 million cash payment — and conveyed the importance of reaching agreement on other terms,” Dr. Garber wrote. “If we can reach agreement on those other terms, we are prepared to invest $500 million in the work force development programs we discussed and I described.”
He added that Harvard’s lawyers had no record of the “proposed edits or additions from the Department of Justice,” but said that the university was “committed to continuing our dialogue and restoring and strengthening the partnership between Harvard and the federal government.”
The government sent revised terms the next day, alarming Harvard officials with seemingly new demands that appeared to encroach on their independence, according to people familiar with the discussions. Harvard privately responded to the government on Tuesday, indicating that the university believed the Trump administration was abruptly seeking to impose new terms and promising a fuller reply after further review.
Harvard officials, already anxious about the prospect of backlash to any settlement with a president many on campus see as autocratic, are sensitive to the details of any agreement.
For months, they have viewed an accord between Brown University and the Trump administration as a model. Under that agreement, Brown agreed to spend $50 million on state work force development programs over a decade. The university did not have to enter into a rigorous monitoring agreement, and it secured a provision that Brown leaders viewed as safeguarding academic independence.
Trump administration officials had initially signaled that Harvard could secure some terms similar to those offered to Brown. But administration officials now contend that Harvard’s troubles in recent years were far graver than Brown’s. Some also point to Harvard’s colossal endowment as a reason that it should pay more.
Harvard has made clear that it is willing to spend more than Brown, but the university’s opposition to treating any portion of that payment as a fine is grounded in its belief that its failures fell short of violations of federal law and are no worse than any other school’s. Some at the university believe that agreeing to a fine would be tantamount to a bribe or an admission of guilt and that it would be depicted that way by detractors — even if a settlement were to explicitly say the university did not acknowledge wrongdoing.
Harvard is not the only university to have grappled this year over the terminology and payment mechanisms that shadow negotiations with the Trump administration.
Columbia University officials ultimately agreed to a $200 million fine after a late-stage demand orchestrated by Mr. Trump.
In November, Cornell and Northwestern each announced agreements with the Trump administration. Cornell agreed to pay the government $30 million and to invest an equal amount “in research programs that will directly benefit U.S. farmers.” And while Northwestern agreed to what was effectively a $75 million fine, it has publicly described the sum as “a settlement fee.”
Mr. Trump has taken a deep interest in the financial components of any settlements, leaving most other details to various aides. A $500 million payment by Harvard would, at least so far, represent the biggest payout by any university to settle with the Trump administration.
But in August, the government stunned the University of California with a demand letter that proposed a $1 billion fine. The university’s president has warned that such a payment would threaten the viability of the 10-campus system, and the Justice Department said in a Dec. 12 court filing that “settlement negotiations are ongoing, U.C. has not accepted any terms and no agreement has been finalized.”
Michael S. Schmidt is an investigative reporter for The Times covering Washington. His work focuses on tracking and explaining high-profile federal investigations.
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