In a searing and emotional meeting Wednesday, faculty members at the Massachusetts Institute of Technology repeatedly challenged the university’s leadership to ensure that the need for research dollars would not blind the university to its fundamental values.

MIT President L. Rafael Reif opened a faculty meeting with an apology, acknowledging that revelations about the school’s ties to the late financier and convicted sex offender Jeffrey Epstein had been disorienting to the campus, and deeply distressing to him. “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,” he said.

“Yet I also know that MIT’s reputation is firmly rooted in the brilliant work that you and our whole community have been doing, and sharing with the world, for decades, and that you will continue to do.”

Some faculty members responded with tears, and some shouted as they debated the university’s past acceptance of funding from Epstein, who pleaded guilty to two felony offenses in 2008, including procuring a person under 18 for prostitution, and was arrested in July on new federal charges of sexually abusing dozens of girls in the early 2000s.

To invite him to visit campus, several people said, was a fundamental betrayal of the women of MIT. “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?” asked a letter signed by more than 50 female faculty members, challenging the administration to back up its rhetoric about inclusion with action.

It was the last straw, some said, in an institutional culture that has long undervalued women.

Some faculty members proposed a resolution that would ensure oversight of donations by faculty members, not just administrators, and transparency about the process. The motion to establish a committee to protect academic integrity will be considered at a faculty meeting in October.

“The values that guide MIT’s faculty, students and staff should never be traded or sacrificed for short term monetary gains or vague promises of future benefit,” the resolution read, in part.

Balakrishnan Rajagopal, an associate professor of law and development who helped write that resolution, said, “MIT needs a lot of internal cleaning up and a fairly significant set of changes to the way it currently operates.”

MIT is not unique, he said. “It’s part of the ecosystem of large universities entangled with all kinds of unholy money everywhere.”

He noted the school has tackled difficult issues head-on in the past.

Faculty members met Wednesday at MIT for their regularly scheduled meeting with only one item on the agenda: the Media Lab.

But the issues involve all of MIT, Reif acknowledged. The school has been roiled by resignations and debates after revelations about the close connection between Epstein and MIT. Ethan Zuckerman, director of the Center for Civic Media at MIT and an associate professor of the practice at the Media Lab, announced last month that he had decided to leave the school at the end of the academic year.

Zuckerman shared updates from the faculty meeting on social media Wednesday and quoted the president of the student body as saying she was angry, and that students felt they had met their moral tipping point.

Hundreds of faculty members filled the room, which was changed this week to accommodate the anticipated crowds.

Some spoke out about the impact of MIT and its research, and called for the institution to look ahead.

A professor defended the fundraising decisions, and asked rhetorically if they should stop the MIT machine.

Some people shouted, “Yes!”

MIT has been roiled by news in recent weeks, including a New Yorker report that Joi Ito, the Media Lab director, and colleagues had sought to conceal Epstein’s donations and relationship with the lab. Ito resigned, and university leaders announced an outside law firm would investigate.

Later that week, Reif announced that senior members of his administration were aware of gifts the Media Lab received between 2013 and 2017 from Epstein’s foundations, and that the investigation had turned up a 2012 letter thanking Epstein for a donation to a mechanical engineering professor. The letter was a standard gift acknowledgment signed by Reif in the early weeks of his presidency, according to Goodwin Procter, the law firm the university had hired to investigate.

“Many students have asked how I could have signed that acknowledgment letter without asking questions, and how I could fail to remember it,” Reif said in prepared remarks Wednesday. “The answer is simple: I did not recognize the name, and I sign many standard thank-you letters every week. That includes several hundred letters every year thanking individuals for contributions to the Institute.”

Reif outlined to faculty members some of the steps the administration was taking, such as efforts to review and correct how it assesses donor agreements. But he acknowledged that the fundamental failure at MIT was in its culture.

“I know that many people have deep concerns about sources we have relied on to raise funds for the work of the Institute,” Reif said. In a time of growing fortunes and shrinking federal funds, administrators need to weigh the political, cultural and economic impacts of donors’ behavior, he said, including examining the issues with anonymous giving. People were telling him, he said, that they needed a set of guiding principles.

“This moment of crisis must be the moment of reckoning,” he said, “and a turn towards real accountability.”