Hundreds of Cambridge students have accused the university of “a complete failure” to deal with complaints of sexual misconduct after an investigation that raised concerns about a conflict of interest among academics.

In a letter signed by more than 500 current and former students, Cambridge University Students’ Union Women’s Campaign has called for colleges to be stripped of their powers to investigate sexual misconduct complaints against their own members.

It comes after it emerged that Dr William O’Reilly, the don then in charge of student welfare at Trinity Hall, Cambridge’s fifth oldest college, appointed a panel to investigate rape allegations against a male student, then gave evidence to the panel in support of the accused.

On Friday night, Trinity Hall announced that both O’Reilly and the college’s master, the Rev Canon Dr Jeremy Morris, were stepping back from their duties until a separate panel of Cambridge fellows issues a report on 2 March on what the college should do.

The letter’s author, Kate Litman, women’s officer at the students’ union, said: “This case is about more than individual failings. It is about an institution-wide failure to protect survivors and tackle sexual violence. That’s why we believe it’s crucial for colleges to commit to a centralised, independent system for handling cases of sexual misconduct.”

Trinity Hall, whose alumni include Stephen Hawking, Rachel Weisz and Geoffrey Howe, is part of Cambridge University’s college system and responsible for its own internal affairs.

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An investigation published last week by the news website Tortoise revealed that three female students told academic staff in February 2018 that they had been raped and sexually assaulted by a male student. He denied the allegations. Two of the women made formal complaints, which were tested at a disciplinary hearing by a panel of dons appointed by O’Reilly, who was Trinity Hall’s acting senior tutor.

According to Tortoise, O’Reilly had a close relationship with the accused student, and gave evidence to the panel. The panel cleared the student of wrongdoing but raised concerns that another academic, Dr Nicholas Guyatt, had acted inappropriately by helping the women to draft their complaints. Guyatt was placed under investigation, and ultimately cleared, but did not regain his pastoral role. He later chose to resign and has become a fellow at another Cambridge college.

Litman’s letter, which is backed by 18 student groups, said: “We believe that the Trinity Hall case shines a light on a broader issue in the collegiate university, and forces us to seriously question the ability of any college to adequately handle sexual misconduct cases. Even if a college has a policy which represents good practice on paper, when complaints are administered by untrained individuals embedded in a close-knit community, there is no guarantee that the policy will be properly followed.”

The row, it added, was not limited to Trinity Hall. “Every college will struggle with conflicts of interest within a relatively small environment, as well as a lack of proper training and expertise. Every year, the Women’s Campaign hears from students who found their case quietly dropped or came up against members of college staff who lacked the knowledge or inclination to support them.”

In a measure of how strongly students feel, more than 220 have signed another letter criticising the history faculty for failing to investigate O’Reilly’s conduct.

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Last year the college was engulfed in a row about Dr Peter Hutchinson, a former fellow, who was the subject of sexual harassment complaints from 10 students in 2015. He was reinstated as a fellow last year, then resigned after an outcry. It emerged last week that in 2015 he had self-published a sexually charged novel under a pseudonym about academics watching students having sex.

A Cambridge University spokesman said: “The faculty takes its safeguarding responsibilities extremely seriously. It regards the welfare of its students as its highest priority. It also has a duty of care to a member of staff who is not under investigation for any offence and who protests his innocence. At the present time, Dr William O’Reilly has voluntarily and temporarily stepped back from his teaching and supervising.”

A spokesperson for O’Reilly said: “Dr O’Reilly believes he acted with integrity and followed appropriate safeguarding advice throughout the various internal processes at Trinity Hall. He rejects any suggestion that he behaved improperly and is appalled that what should have been confidential procedures have been made public.”

• This article was amended on 23 February 2020 to clarify details of the investigation concerning Dr Nicholas Guyatt, in which he was exonerated, and the circumstances of his later resignation.