But in recent days, the globe-trotting Ito has found himself in the midst of a crisis that is tearing at the lab he has helped to elevate since taking it over in 2011 at age 44.

This month, Ito acknowledged that he had extensive personal and professional ties to Jeffrey Epstein, the disgraced financier who committed suicide in prison Aug. 10 while facing federal charges of sex trafficking of underage girls.

Since then, a well-known professor and a visiting scholar have both announced they will quit the lab in protest. Students inside the lab have demanded a fuller accounting of Ito’s relationship with Epstein. And a current graduate student and former research associate have called on Ito to resign, saying the apology he posted online is not enough.

“Joi isn’t a bad person, but he can’t lead us,” said Arwa Mboya, 25, a graduate researcher studying imagination and technology who is entering her second year at the lab. Despite questions and concerns raised by students, Ito hasn’t offered a complete explanation of why he got involved with Epstein.

“He has not been transparent about who, when, and why,” Mboya said.

Late Thursday, MIT president L. Rafael Reif said the school had received about $800,000 over two decades via foundations controlled by Epstein, and he apologized to Epstein’s victims on behalf of the administration. Reif also convened a committee to investigate the Epstein donations.

Ito did not respond to requests for comment.

In his public apology, Ito said he had traveled to Epstein’s homes and accepted money from him for both the research center and Ito’s own investments into tech startups. Ito said he first met Epstein in 2013, five years after Epstein had pleaded guilty to soliciting a minor for prostitution and served a year in jail.

“I take full responsibility for my error in judgment,” Ito wrote, adding that he would raise an equivalent amount to what Epstein gave the Media Lab and donate it to nonprofits that work with survivors of human trafficking.

He also promised to return the money Epstein invested in his funds.

Ito did not explain the purpose of his visits to Epstein’s homes; however, he said he was “never involved in, never heard him talk about, and never saw” evidence of Epstein’s alleged crimes.

The revelation has shaken an institute that has deep corporate connections and is credited with innovations that range from the electronic ink in tablet readers to new technology that helps children learn computer programming.

Founded in 1985, the Media Lab holds a unique place on MIT’s campus.

It is home to more than 30 faculty and senior researchers and 275 other students and staff. Its $80 million budget is funded primarily by corporate giants including IBM, ExxonMobil, and Google, which gain broad access to the lab’s research.

“We could work on whatever we thought was important,” said Walter Bender, a founding member and former director of the lab, who left in 2006. “That was a tremendous change from MIT’s traditional approach to academics.”

The lab’s funding formula gives its researchers almost limitless freedom to explore areas ranging from digital currency to the future of food and the ethics of technology.

“It was much more serendipitous, and you could go off and chase a wild idea,” Bender said.

Ito was an unconventional choice to lead the lab. A two-time college dropout, from Tufts University and the University of Chicago, he had a successful career as an Internet entrepreneur in Japan, where he was born.

Ito was also an early investor in Twitter, Flickr, and Kickstarter.

According to a nonprofit tax filing by an MIT affiliate, Ito earned $327,640 in 2017.

“Ito was a little bit of a breath of fresh air,” Bender said. “He comes from very much of a business focus, an entrepreneurial focus, and that certainly had an impact on the lab.”

Ito’s investment background and expansive global network also helped the lab raise money and even launch its own venture capital fund.

But his fund-raising has sometimes been controversial. The lab recently cut ties with the private foundation run by Saudi Crown Prince Mohammed bin Salman, who toured the lab last year during an MIT visit, before he was accused of ordering the killing of the journalist Jamal Khashoggi, according to The New York Times Magazine.

Ethan Zuckerman, director of the lab’s Center for Civic Media, who recently announced that he is resigning from the lab in 2020 in protest, said he warned Ito in 2014 not to meet with Epstein.

Epstein had courted prominent academics at other institutions, including Harvard, and had expressed interest in the Media Lab several years before Ito arrived.

Epstein “was sniffing round the lab even when I was there,” Bender said. “He was making noises about funding some research” in artificial intelligence.

Bender said he never met Epstein and was not aware of any donations accepted from the financier during his tenure as director.

Controversies about the ethics of accepting money from certain companies or individuals sometimes occurred at the lab, Bender said. But Ito, by taking money from Epstein for the lab as well as his own private investments, “muddied a line that I worked hard to avoid,” Bender said.

Ito continues to have support among several students and staff at the Media Lab.

Habib Haddad, a friend of Ito’s who has known him for 10 years and helps run the lab’s venture fund, said he has heard from many students and faculty who want Ito to remain in place.

“While they are sad and disappointed at Joi’s mistakes, they don’t want Joi to go and believe he is the right leader to put in place corrective measures and lead the lab,” Haddad said. “There is an overwhelming majority — one could say silent majority — that is in support of Joi staying and leading the lab through this.”

Other students and scientists at the lab said they are disappointed by the social media-driven effort to push Ito out and believe he should be given a chance to make corrections and help MIT better evaluate when to accept donor funds.

But Kim Holleman, a New York City artist who was a research affiliate at the Media Lab from 2013 to 2017, said last week that Ito must resign.

“Anyone who took any money from Epstein, for whatever reason, has taken rape money,” Holleman wrote on Medium. “How on earth can anyone claim to be an intelligent person, smart enough to run MIT Media Lab, but not be smart enough to know the difference between right and wrong?”

Deirdre Fernandes can be reached at deirdre.fernandes@globe.com. Follow her on Twitter @fernandesglobe. Michael Levenson can be reached at mlevenson@globe.com. Follow him on Twitter @mlevenson.