The former head of an elite Brisbane school has denied he had an attitude of dismissing and ignoring persistent complaints about two pedophile staff members.

Gilbert Case was the principal of St Paul's from 1979 to 2000, during which time both Kevin John Lynch and Gregory Robert Knight worked at the school.

The child sex abuse royal commission has heard Lynch horrifically abused scores of boys at the school, as well as Brisbane Grammar, including drugging them and inserting needles into their genitals.

It's believed he had up to 1000 appointments with students throughout the school year in his office, which was rigged with a 'traffic lights' system to stop people stumbling in unannounced.

In their testimonies, some of his victims have accused Mr Case of dismissing and threatening them when they complained about Lynch.

One former student even claimed he went to Mr Case in 1996 after enduring a five-hour ordeal with the depraved counsellor only to receive a blunt denial.

Counsel assisting David Lloyd on Thursday pressed the ex-headmaster about this and suggested he had an attitude of rejecting and failing to investigate allegations levelled at both former staff members, excluding concerns raised in a school council meeting in October 1984.

'No, and there were no allegations about Lynch during his lifetime,' Mr Case maintained.

He said he'd 'searched memory and heart' as he listened to two victims recall their account of a 1996 meeting.

'I found it difficult listening to them because I almost wanted to believe them,' he said.

The inquiry also heard Mr Case had a handwritten, undated note listing allegations Knight had played a game 'in (the) raw' with students and cupped another's penis and testicles.

But earlier in his evidence, the ex-principal said he probably didn't think of a male teacher fondling a student's penis 'in terms of criminal acts'.

Knight was allowed to resign from the school in late 1984 after sexual abuse claims.

Mr Case admitted a reference he later wrote for the former employee - who went on teach in the Northern Territory and be jailed for child sex offences - was a 'stupid thing' to do.

'I can only apologise to the commission and to any students anywhere in Australia or anywhere else who was affected as a result,' he said.

He said he'd informed the school council Knight had been dismissed despite him actually resigning, deeming the distinction a case of 'splitting hairs'.

The royal commission has previously heard a student wore a wire to Lynch's home, setting in motion a chain of events that led to him being charged with nine counts of child sex offences in January 1997.

He killed himself the next day.

The royal commission continues.

AAP