A Geelong Grammar School chaplain hypnotised boys so he could molest them, boarders were sexually abused as they slept and students were subjected to incessant bullying and even abuse by their peers, an inquiry has heard.

A code of silence discouraged students from reporting five decades of abuse which continued until as recently as 2007 while those who did speak out were met with inaction or even threatened with expulsion, the child abuse royal commission heard.

Victim BKO has told the commission that Rev John Davison abused him during one of two after-school sessions in 1970 in which the school chaplain tried to hypnotise a group of students.

BKO reported the incident to teacher Jonathan Harvey - who was later convicted of abusing a student - and was told he may be expelled.

Former student Dr Robert Llewellyn-Jones said Rev Davison, now deceased, also tried to hypnotise him in 1971.

"He told me he could teach me about sex and that I could do it with him so that I would get very good at it," the Sydney psychiatrist told the commission on Tuesday.

When Dr Llewellyn-Jones yelled for him to stop, Rev Davison threatened to tell the deputy headmaster that the 15-year-old had propositioned the chaplain.

Dr Llewellyn-Jones said he did not disclose the bullying and sexual and physical abuse he suffered because of a deep code of silence embedded in the school's culture.

"In my opinion, the power and prestige of the school served to discourage victims from breaking their silence about the abuse they experienced," he said.

Bullying victim BKU said chaplain Rev Norman Smith twice abused him at the Timbertop rural campus, where he spent year 10 in 1967, noting it was a year after Prince Charles's stint there.

"The environment at Geelong Grammar was so heavily steeped in a punishing culture devoid of pastoral care that I never raised the issues while at school," BKU said.

BKU said a Geelong Grammar teacher and historian, who was also Prince Charles's personal tutor, defended the school as a noble institution after a brother's torrid time at the school was mentioned in a eulogy at his funeral.

Counsel assisting the commission David Lloyd said very senior staff knew about child abuse allegations at or about the time the abuse occurred, including against live-in boarding house assistant Philippe Trutmann who abused 40 students.

"After these matters came to the attention of the school between 1985 or 1986 and 1992, Trutmann went on to sexually abuse more children at the school," Mr Lloyd said.

He said Trutmann, called "filthy Phil" by some of the boys, would regularly go into boys' rooms at night when they were asleep and sexually abuse them.

"Sometimes the boys did not wake. At other times they were awake but did not move because they were frozen with fear," Mr Lloyd said.

The commission heard one student who reported being sexually abused in his room was told not to talk about what happened and was expelled after discussing the matter with another student.

Mr Lloyd said there is no record of any investigation into that student's allegations and no report to police.