A letter signed by more than 60 of the Massachusetts Institute of Technology’s (MIT) leading female faculty members outraged over donations from Jeffrey Epstein, and the wider professional culture at the elite institution, was handed to the university’s president, L Rafael Reif, on Wednesday.

The letter described the decision by MIT to court, accept and then disguise donations from Epstein, a financier and convicted sex offender, as “profoundly disturbing” ahead of a heated two-hour faculty meeting.

The Wednesday meeting came as almost daily disclosures reveal the extent of the university’s relationship with Epstein, who committed suicide in a jail in New York last month while facing fresh charges of sex trafficking girls as young as 14.

The meeting was called as female faculty members sought to question the school’s commitment as a whole to female academics.

It came two days after the male faculty member Richard Stallman resigned, after sending an email to colleagues saying that one of Epstein’s alleged victims had presented herself as “entirely willing” to have sex.

The scandal sweeping though MIT has also embroiled female academics, with the Media Lab professor Neri Oxman apologising and saying: “I regret having received funds from Epstein, and deeply apologize to my students for their inadvertent involvement in this mess.”

In a statement, Oxman said she had been told to keep the $125,000 donation in 2015 confidential, “so as not to enhance [Epstein’s] reputation by association with MIT”.

At the meeting on Wednesday, reported the Boston Globe, Reif offered a new apology that acknowledged that the university’s culture had led it to take money from a convicted sex offender.

“I am deeply sorry,” Reif said, according to a statement released by the university. “I understand that I have let you down and damaged your trust in me and that our actions have injured both the institute’s reputation and the fabric of our community.”

In his first first face-to-face encounter with faculty since the Epstein scandal broke, Reif acknowledged that the “tech world in general, devalue the lives, experiences, and contributions of women and girls” and said he understood it was a “last-straw moment”.

“I am humbled that it took this cascade of misjudgments for me to truly see this persistent dynamic and appreciate its full impact. It’s now clear to me that the culture that made possible the mistakes around Jeffrey Epstein has prevailed for much too long at MIT,” he added.

Epstein, who was found dead in his jail cell after being arrested on sex trafficking charges, donated almost $10m to MIT over two decades, with many of the gifts coming after he registered as a sex offender in Florida in 2008.

MIT has announced a review of how it evaluates donors and whether the university’s policies need to change.

But many female members of the faculty and former assistants at the lab point to broader gender equity problems.

“How can MIT’s leadership be trusted when it appears that child prostitution and sex trafficking can be ignored in exchange for a financial contribution?” the letter read, and called the chain of decision-making around Epstein “profoundly disturbing”.

They pointed to inequities in both gender and race. This year only 266 of 1,066 faculty members are women, and only 21 are women of color, according to the letter. “Members of our community have been left feeling undervalued, deceived and unsafe,” the letter said.

Last week, former fundraiser Signe Swenson told the Guardian that if any good can come out the scandal it will be when MIT starts listening to women in the faculty.

“I saw women at the lab speak out and their word meant nothing because Joi [Joi Ito, its former head] refused to admit the truth,” Swenson said.

Ito resigned earlier this month.

“For those women who stuck around, I hope they are given some control and influence over the Media Lab and to shape it into something more equitable and safe. If they just start listening to the women it’ll be a very different place,” Swenson added.