The director of MIT’s prestigious Media Lab stepped down Saturday after an outcry over his financial ties with the disgraced financier Jeffrey Epstein, whose contributions to the proudly contrarian lab roiled and divided its members.

“After giving the matter a great deal of thought over the past several days and weeks, I think that it is best that I resign as director of the media lab and as a professor and employee of the Institute, effective immediately,” the director, Joichi Ito, wrote in an email to the provost of the Massachusetts Institute of Technology, Martin A. Schmidt.

Ito acknowledged this past week taking $525,000 of Epstein’s money for the lab, as well as $1.2 million for his personal investment funds. He stepped down less than a day after an article in The New Yorker described the measures that officials at the lab took to conceal its relationship with Epstein, who killed himself in jail last month while facing federal sex trafficking charges.

In a separate email to the lab community, Ito again apologized. “While this chapter is truly difficult, I am confident the lab will persevere,” he wrote.

Ito shared the emails with The Times after repeated requests for comment. He was a board member of The New York Times Co. since 2012, but on Saturday, the company announced that he had resigned from the board.

Ito, who took over the Media Lab in 2011, had enjoyed strong support inside the lab, where he had helped raise more than $50 million in donations over the years. But the revelations in The New Yorker article eroded his support. Names began disappearing Saturday from an online petition in support of him that had been put up last month.

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The internal lab emails, which a former lab employee shared with The New York Times, described donations that Epstein made and solicited over the years — including from Leon Black, founder of the private equity firm Apollo Global Management, and a $2 million gift from Microsoft co-founder Bill Gates.

In an email in October 2014 — six years after Epstein had pleaded guilty to a sex charge involving a minor in Florida — Ito wrote that the gift from Gates was “directed by Jeffrey Epstein.” Peter Cohen, then a development official at the lab, wrote in a subsequent email, “For gift recording purposes, we will not be mentioning Jeffrey’s name as the impetus for this gift.”

A spokesman for Gates issued a statement Saturday afternoon, saying: “Epstein was introduced to Bill Gates as someone who was interested in helping grow philanthropy. Although Epstein pursued Bill Gates aggressively, any account of a business partnership or personal relationship between the two is simply not true. And any claim that Epstein directed any programmatic or personal grant making for Bill Gates is completely false.”

Cohen, now the director of development for computer and data science initiatives at Brown University, did not respond to messages seeking comment Saturday.

Signe Swenson, who served as a development associate and alumni relations coordinator at the lab from 2014 to 2016, shared the internal emails concerning Epstein with The Times. She said she had told supervisors at the lab several times of her “disgust” at Epstein’s involvement with the lab.

“That was never listened to,” Swenson, who worked under Cohen, said in an interview on Saturday that also included an attorney from the group Whistleblower Aid.

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Swenson said she learned of Epstein’s connection with the lab when she interviewed for a position in March 2014. She said she later told Cohen that MIT listed Epstein as “disqualified” as a donor, but Cohen replied that Ito had a relationship with the wealthy financier.

In one 2014 email shared by Swenson, Ito wrote about a $100,000 donation from Epstein, asking the development staff members to “make sure this gets accounted for as anonymous.” Cohen wrote in a subsequent email that the donation was “Jeffrey money, needs to be anonymous.”

Other emails suggest that Epstein sought out donations from others. In the correspondence about the donation from Gates, Cohen wrote that Ito “did not talk with Bill Gates” and that the lab “did not solicit this money.”

Ito acknowledged receiving money from Epstein in an online apology on Aug. 15. That prompted MIT to begin an internal review.

On Saturday, the university’s president, L. Rafael Reif, said he had asked MIT’s general counsel to hire an outside law firm to conduct “an immediate, thorough and independent investigation.”

“The acceptance of the Epstein gifts involved a mistake of judgment. We are actively assessing how best to improve our policies, processes and procedures to fully reflect MIT’s values and prevent such mistakes in the future,” he wrote in an email to the university community. “Our internal review process continues, and what we learn from it will inform the path ahead.”

One series of emails, from May 2014, indicated that Epstein also helped connect the lab to Black of Apollo, who Epstein had advised on issues including philanthropy.

Cohen wrote that Black wanted to make a large donation “in honor of a friend, who wishes to remain anonymous,” and later asked Ito to find out from Epstein whether Black himself wanted to remain anonymous. One email indicated that Black had given the lab a gift of $4 million by wire transfer.

Cohen also asked Ito whether Black would like a thank-you note from MIT’s president. Black’s preference would be something “you or Jeffrey knows best,” be wrote.

A spokeswoman for Black did not immediately comment Saturday. Black has sought to distance himself from Epstein, describing his interactions with him as limited to tax strategy, estate planning and philanthropic advice. He has also said Apollo, one of the world’s largest private equity firms, had never done business with Epstein.

Some colleagues at the lab had called for Ito to step down, questioning his judgment for taking contributions from Epstein. Two scholars said they would leave the lab at the end of the academic year because of them, and one of said he had urged Ito not to associate with Epstein.

The meeting last Wednesday was intended to help bolster support for Ito. He told the crowd that he had “screwed up” by accepting the money, but that he had done so after a review by the university and consultation with his advisers.

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But near the end, one of Ito’s staunchest supporters, Nicholas Negroponte, a founder of the lab, said he had told Ito to take the money and would do it again. That prompted Ito to send an email to Negroponte in the middle of the night, complaining that he was undercutting his ability to make amends.

Ito also held board positions and advisory roles at a number of organizations, including the John S. and James L. Knight Foundation and the MacArthur Foundation. On Saturday afternoon, the MacArthur Foundation said that Ito had resigned from its board, adding, “The recent reports of Ito’s behavior in The New Yorker, if true, would not be in keeping with the values of MacArthur.”

A spokesman for the Knight Foundation, Andrew Sherry, said on Saturday that Ito had resigned from its board as well.