Presidents of Harvard University and the Massachusetts Institute of Technology acknowledged in separate announcements this week that their connections to financier Jeffrey Epstein went deeper than previously revealed, further entangling the elite institutions with a donor who was a convicted sex offender.

At MIT, senior officials knew of gifts from Epstein and sought to ensure those donations remained anonymous, the school’s president, L. Rafael Reif, wrote in a letter to campus. Reif also said an investigation had turned up a 2012 letter signed by Reif thanking Epstein for a donation.

Harvard officials revealed that the university had accepted about $9 million in donations from Epstein between 1998 and 2007, and announced intentions to redirect some of the unspent money to organizations helping victims of trafficking and sexual assault.

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Epstein pleaded guilty in 2008 to two felony offenses, including procuring a person under 18 for prostitution. Epstein was arrested in July on new federal charges of sexually abusing dozens of girls in the early 2000s. In August, he was found dead while in federal custody.

The revelations raised questions from faculty, students and the public about how some of the world’s most admired institutions raise money and whether the school’s leaders are appropriately transparent about relationships with major donors.

In a letter to the campus Thursday, Harvard President Lawrence S. Bacow said the school rejected a donation offered by Epstein after 2008, the year when Epstein was convicted on sex charges. Bacow wrote that a review has not found gifts accepted after Epstein’s conviction.

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“The issue of the gifts given to institutions by donors at Jeffrey Epstein’s suggestion, is also one that has emerged in recent days,” Bacow wrote, “and we are looking into this as part of our ongoing review.”

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Emails first published in the New Yorker and shared with The Washington Post by the nonprofit Whistleblower Aid suggested that employees of the MIT Media Lab sought to conceal gifts from Epstein years after his conviction and apparently accepted gifts from other donors who had been “directed” by Epstein to the Media Lab.

“Jeffrey money, needs to be anonymous,” Peter Cohen, then the director of development and strategy for the MIT Media Lab, wrote in a 2014 email.

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Signe Swenson, who worked in development for the Media Lab at that time, said she and some of her colleagues were uncomfortable about the relationship, especially when Epstein visited the Media Lab. “It became so real to myself and everyone in the office what that relationship meant,” she said, “. . . and how distressing it was to have him there.”

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She left MIT and decided to disclose information after “watching MIT carefully avoid the truth,” she said.

Cohen said he did not witness anything he believed to be illegal, did not solicit gifts from Epstein, had no personal relationship with him and had only a few limited personal interactions with Epstein.

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“I, like others, am disgusted and distraught by Jeffrey Epstein’s conduct,” Cohen said in a written statement. He said that when he joined MIT in 2014, there were gift-acceptance policies and practices for Epstein, “which I understood were authorized by, and implemented with the full knowledge of, MIT central administration. Notwithstanding my personal discomfort regarding Mr. Epstein and his involvement with MIT, I did not believe I was in a position to change MIT’s policies and practices.”

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Cohen was put on administrative leave this week from his job at Brown University, where he began working in October.

“Brown has not in its history received any funds from Jeffrey Epstein,” university spokesman Brian Clark said in a written statement. “We are engaged in a review of available information regarding Mr. Cohen in the context of Brown University policies, core values and the University’s commitment to treat employees fairly.”

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After the allegations about concealment of Epstein’s role became public, Joi Ito, the Media Lab director, resigned and the school announced a law firm would investigate the extent of the connections between MIT and Epstein.

Reif told the campus the investigation had turned up a 2012 letter signed by Reif thanking Epstein for a donation to Seth Lloyd, a mechanical engineering professor. The letter was a standard gift acknowledgment signed in the early weeks of his presidency and he does not remember it, Reif wrote.

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In 2013, when senior members of Reif’s team learned of the first gift to the Media Lab, Ito asked for permission to keep the donation, Reif wrote.

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“They knew in general terms about Epstein’s history — that he had been convicted and had served a sentence and that Joi believed that he had stopped his criminal behavior,” Reif wrote. “They accepted Joi’s assessment of the situation. Of course they did not know what we all know about Epstein now.”

Ito sought the gifts for general research, Reif wrote: “Because the members of my team involved believed it was important that Epstein not use gifts to MIT for publicity or to enhance his own reputation, they asked Joi to agree to make clear to Epstein that he could not put his name on them publicly. These guidelines were provided to and apparently followed by the Media Lab.”

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Epstein’s gifts were discussed during at least one of MIT’s regular senior team meetings and Reif was present at the meeting, according to the update given to MIT leaders by Goodwin Procter, the law firm hired by MIT to investigate.

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Reif wrote that “we could and should have asked more questions” about Epstein. “We did not see through the limited facts we had, and we did not take time to understand the gravity of Epstein’s offenses or the harm to his young victims. I take responsibility for those errors.”

At Harvard, Bacow noted the university’s decentralization makes a review of donations more complicated than it would be at some other institutions.

Most of the gifts from Epstein were designated for current use on research and education and were spent years ago, Bacow wrote. The largest gift, $6.5 million, was given in 2003 for the Program for Evolutionary Dynamics and spent by 2007, according to the university.

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The ongoing review identified a current-use fund and a gift to the Faculty of Arts and Sciences with an unspent balance of $186,000, Bacow noted, and university officials have decided to donate that amount to funds benefiting victims of trafficking and sexual assault.

“This is an unusual step for the University,” Bacow wrote, “but we have decided it is the proper course of action under the circumstances of Epstein’s egregiously repugnant crimes.”

Bacow also noted that Stephen Kosslyn, a former faculty member who benefited from donations from Epstein, designated Epstein as a visiting fellow in the Department of Psychology in 2005, and that officials were working to learn more about that appointment.

Kosslyn did not respond to a request for comment.

“Epstein’s behavior, not just at Harvard, but elsewhere, raises significant questions about how institutions like ours review and vet donors,” Bacow wrote. He said he would convene a group at Harvard to consider how to prevent such situations, and expressed hope that peer institutions could collaborate on solutions.

“Jeffrey Epstein’s crimes were repulsive and reprehensible. I profoundly regret Harvard’s past association with him. . . .

“Harvard is not perfect, but you have my commitment as president that we will always strive to be better.”

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