A former principal of a Brisbane school has told a royal commission that he did not consider sexual abuse of pupils by teachers to be a criminal matter.

The inquiry is examining the conduct of two men, former music teacher and convicted paedophile Gregory Robert Knight and former school counsellor Kevin John Lynch, who both worked at St Paul's School at Bald Hills during the 1980s and 1990s.

Gilbert Case was the headmaster at St Paul's School for 20 years, during which time staff members, Knight and Lynch, sexually abused students during the 1990s.

It has been alleged Case knew about Knight's abuse of students and took no action.

Under questioning at the Royal Commission into Institutional Responses to Child Sexual Abuse, Mr Case said he had not thought sexual assault was a criminal matter.

"If the behaviour of the adult teacher extended to the adult teacher touching or fondling the genitals of students in their care, that would plainly be a criminal act?" counsel assisting David Lloyd asked.

Mr Case replied: "I probably did not think of that in terms of criminal acts".

"I believe I've said in my statement [to the royal commission] that the first time that was suggested to me was in a conversation with [a police detective] in 2002," Mr Case said.

The commission heard Knight was asked to leave his previous teaching job at Brisbane Boys' College (BBC) at Taringa after allegations of improper behaviour.

But Mr Case has told the commission he spoke with the principal of BBC, Graeme Thomson, before employing him at St Paul's and there was no mention of allegations at BBC.

"He said nothing that led me to believe that any student would be at risk if Mr Knight were employed at St Paul's," Mr Case said.

Earlier this week Mr Thomson testified he did warn Mr Case about hiring Knight.

'I wrongly assumed I knew Kevin Lynch better'

Mr Case denied allegations from counsel assisting the commission of trying to sweep allegations about Lynch under the rug, but said: "I wrongly assumed I knew Kevin Lynch better than I did."

Kevin Lynch took his own life in 1997, a day after being charged with child sex offences. ( ABC News )

Mr Case worked at BGS in 1971 and that was where he met Lynch.

Mr Case became principal of St Paul's in 1979.

Victims have given evidence that they told Mr Case they were being abused, but said he dismissed them and threatened them with punishment.

Several victims have testified that Lynch drugged them, hypnotised them and performed sexual acts on them.

Students have also said that they felt Mr Case was shielding Lynch because the pair were close friends.

Witnesses have told the commission they felt let down by Mr Case.

Mr Case on Thursday accepted that during his 20-year tenure he did not institute any policies to deal with sexual abuse.

Paedophile teacher had red light outside door

The commission has heard evidence about how Lynch had a lighting system outside his door - and that a red light meant you could not enter.

Mr Case also testified the counselling room's door locked and that Lynch was asked to keep his door ajar, but that the edict was not enforced.

Mr Case told the commission he was angry with a number of people, including himself and Mr Lynch, following his death.

Lynch took his own life in 1997, a day after being charged with child sex offences.

Mr Case was interrupted from the public gallery when he started to describe the circumstances.

"He had grossly and maliciously played on ..." he said, when a man yelled from the public gallery: "Tell the truth."

Mr Case then said he regarded the victims as courageous and determined young men.

"I can only apologise to these people and admire their courage now," he said.

"We have a situation where there is a teacher who has been trusted. The teacher who has been trusted has obviously been wrongly trusted, and the events that came to light, and the fact that they were slow in coming, was part of the difficulty.

"And I congratulate [former students and witnesses at the inquiry] BSB and BRC on helping to bring all that to light."

Teachers 'forbidden from talking'

Multiple victims have given evidence they were molested by Lynch throughout the 1990s.

Lynch took his own life in 1997, a day after being charged with child sex offences.

Earlier the inquiry heard that teachers at a Brisbane school were forbidden from talking about allegations of sexual assault.

Former teacher Craig Patterson told the inquiry there were rumours circulating about Lynch's activity but he was directed to not talk with anyone about it.

"We'd been told - the staff - had been forbidden from talking about Lynch," he said.

In his written statement to the commission, Mr Patterson said he had not been aware of the extent of the allegations against Lynch.

"I could not understand the position the school was taking in not addressing the rumours and forbidding any discussion or mention of his name," he said.

"I, and I feel many of the other staff at St Paul's, were simply confused and in the dark - we had so many questions and no answers."

Mr Patterson said despite his lack of knowledge of any of Lynch's wrongdoing prior to his death, he would always feel that "I failed in my duty because I did not see the monster in front of me".

"I feel that I should have saved the children in my care from him," he said.

"I am ashamed and sorry that I was helpless in my ignorance, both before and after his horrible acts of abuse - I apologise to you boys.

"The silent compliance and lack of outrage by many of my colleagues, and the flippancy of a few over the issue of child sexual abuse, left me hurt and disillusioned about the teaching profession and human nature."

He said some of those in charge of schools chose to protect the institution, rather than the children.

"All too often those in charge of schools lose sight of this duty and instead come to focus on the institution itself rather than the very purpose for its existence," he said.

"So desperate are they to protect the institution and themselves within it, that this loss of focus allows monsters to not only creep in and hide, but to thrive.

"Any toleration of a monster's presence, even if it is to put one's head under the blankets and pretend it does not exist is inexcusable."

"The truly brave are the victims who turn from their horror and wounds to face the monsters down - all of us should stand with them."

Headmaster asked Knight to resign

Mr Case has apologised to students who were affected as a result of the reference he wrote for Knight, who went on to teach at a school in the Northern Territory following his resignation from St Paul's.

Giving evidence at the inquiry, Margaret Goddard, who took over from Mr Case as headmaster, said that during a handover meeting Mr Case told her why Knight had left the school.

Mr Case intimated to Ms Goddard that Knight had dealt inappropriately with students and he had asked the teacher to resign.

Knight subsequently resigned from St Paul's and moved to the Northern Territory to work at Darwin's Dripstone High School, where serious allegations of child abuse were made against him in 1993.

She also claimed Mr Case said he wrote a letter of recommendation to help Knight gain employment in the NT.

The school and the NT Department of Education refused Knight's offer to resign, with the school sacking him on the spot.

On Thursday, Mr Case offered an apology.

Gregory Knight gave evidence to the child sex abuse royal commission via video link. ( AAP Image: Dan Peled )

"I can only apologise to the commission and to any students anywhere in Australia, or anywhere else, who were affected as a result of my writing this reference," he said.

"I believe it was a stupid thing to do and something I should not have done."

Mr Lloyd, counsel assisting the commission, then put to him: "It was reckless, wasn't it?"

To which Mr Case replied: "I would agree with you."

Mr Lloyd: "In total and utter disregard for the welfare of any student at a school that Knight may have come to be employed at in light of what you knew about him?"

Mr Case: "I would now agree with you."

In 1994, Knight was convicted and sentenced to eight years in jail with a three-year non-parole period for child sex offences in the NT.

In 2005, he was convicted of sexually abusing a former St Paul's student, identified at the inquiry as BSG.

This week, Knight gave evidence to the royal commission, accusing students of making up stories about him after he was convicted of a child sex offence.