The president of the Massachusetts Institute of Technology has ordered an independent investigation of the ties between a prestigious research lab at the school and Jeffrey Epstein, the influential financier and convicted sex offender.

Joi Ito, the director of the influential MIT Media Lab, submitted his resignation on Saturday, in the wake of continued scrutiny over the center’s financial relationship with Epstein, the university announced in a statement.

Ito, who was also a member of the New York Times Company board of directors, also resigned from that board, “effective immediately”, a Times spokeswoman said.

MIT and the Media Lab had previously admitted to accepting some financial donations from Epstein, despite the financier’s public history of pleading guilty to soliciting prostitution from a child.

But new reports from the New Yorker and the New York Times said that internal emails indicated Media Lab officials had worked to conceal the full extent of Epstein’s donations to the Media Lab, and his other assistance to the center.

This included at least $7.5m in donations Epstein helped secure from two other prominent philanthropists, Bill Gates and the investor Leon Black, the New Yorker reported.

In a statement, MIT’s president, L Rafael Reif, called the allegations in the New Yorker story “deeply disturbing” and “extremely serious” and pledged that the university would conduct “an immediate, thorough and independent investigation”, which would be conducted by a “prominent law firm”.

“The acceptance of the Epstein gifts involved a mistake of judgment,” Reif wrote. The university was still assessing how to “prevent such mistakes in the future”.

The New Yorker’s investigation cited former media lab employees who spoke about their concerns about the lab’s years-long relationship with Epstein, as well as internal emails from Ito, who wrote of one Epstein donation: “Make sure this gets accounted for as anonymous,” and another from an employee who wrote: “Jeffrey money, needs to be anonymous.”

In 2015, according to Signe Swenson, a former development associate at the lab who spoke to the New Yorker, Epstein himself visited the lab, accompanied by two young female “assistants”.

Swenson said the visit, already uncomfortable, became more distressing at the sight of the young women who accompanied Epstein.

Among the lab’s staff, “all of us women made it a point to be super nice to them. We literally had a conversation about how, on the off chance that they’re not there by choice, we could maybe help them,” Swenson told the New Yorker.

The lab’s internal planning for the visit included ensuring Epstein’s name was kept off Ito’s public calendar, and strategizing about how to keep a member of the lab who disapproved of its association with Epstein from seeing the meeting in progress, Swenson told the New Yorker.

Ito, who led the influential university research center for eight years, emailed his resignation to university officials on Saturday, according to the New York Times.

“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,” Ito wrote in an email shared with the New York Times.

Ito did not immediately respond to requests for comment.

The investor and author has been an influential figure in the world of American media, technology and philanthropy. As well as having served on The New York Times board, he had been serving on the board of the Knight Foundation, one of the most prominent funders of media innovation in the United States; and the MacArthur Foundation, which has given out grants totalling nearly $70bn in the past decades.

In a tweet on Saturday, the MacArthur foundation announced that Ito had also resigned from its board.

“The recent reports of Ito’s behavior in The New Yorker, if true, would not be in keeping with the values of MacArthur. Most importantly, our hearts go out to the girls and women who survived the abuse of Jeffrey Epstein,” the foundation tweeted.

The public revelations about Epstein’s relationships with MIT’s Media Lab had been divisive, with some Lab members and associates defending the center and others calling its ties to Epstein unacceptable. Before the New Yorker story was published, some of Ito’s friends and associates publicly came to his defense.

MIT’s president said the university had taken about $800,000 from Epstein over 20 years. The New Yorker reported Epstein had arranged $7.5m in donations.

Epstein killed himself in jail on 10 August while awaiting trial on sex trafficking charges.

Just days ago, a co-founder of the Media Lab had defended its decision to accept hundreds of thousands of dollars in funding from Epstein.

“If you wind back the clock, I would still say ‘take it’,” Nicholas Negroponte said at a town hall meeting on Wednesday.

Negroponte, whose brother served as an assistant secretary of state under George W Bush, later defended his remarks to the Boston Globe.

“We all knew he went to jail for soliciting underage prostitution,” Negroponte told the Globe. “But we thought he served his term and repented.”

In 2008, Epstein pleaded guilty to a charge of soliciting prostitution from an underage girl, as part of a lenient deal with federal prosecutors in Florida. He served 13 months of an 18-month prison sentence, much of it on day release.

That plea deal came under renewed scrutiny in recent months following a series of articles published by the Miami Herald, leading to new charges being filed against Epstein by federal prosecutors in New York.

Alex Acosta, who as US attorney in Miami oversaw the deal, resigned as US labor secretary.

The Associated Press contributed to this report