A former principal admits that evidence he gave to a trial and Royal Commission about the same sex abuse case is inconsistent.

The Catholic Church has accused a former principal of lying under oath about a child sex abuse scandal at his primary school.

Terence Hayes has admitted he didn’t tell police, superiors or parents the full truth about allegations against pedophile teacher Gerard Byrnes in 2007 and 2008.

But Mr Hayes also admitted to the Royal Commission into Institutional Responses to Child Sexual Abuse on Wednesday that he knew at the time he had an obligation to tell police.

He was first told of serious sexual abuse allegations against Byrnes in September 2007, but kept them secret from parents and police until the teacher was arrested in November 2008.

Mr Hayes himself was tried in 2009 for failing to pass on the allegations to police.

He was found not guilty after proving he understood his instructions were to report sex abuse claims only to superiors at the Catholic Education Office.

However, under a savage and unrelenting cross-examination by Jane Needham for the Church, Mr Hayes admitted on Wednesday he had been told by superiors that he was obligated to report any child sex abuse claims to police.

Ms Needham asked Mr Hayes if he understood that those two positions were fundamentally inconsistent.

“Yes,” he replied.

Ms Needham then put to the former principal that he lied during his 2009 trial and then made up stories to pass on blame and get himself out of trouble at the Royal Commission.

“I deny that,” Mr Hayes said.

Ms Needham said: “I put to you that you are quite prepared to make things up to suit whatever situation you find yourself in”.

“I categorically deny that,” he replied.

But it is understood that counsel assisting could refer Mr Hayes, who still works as a Catholic school teacher, to the Department of Public Prosecutions over his inconsistent evidence.

Mr Hayes agreed his failure to report Byrnes, even though he thought he was a risk to students, amounted to gross incompetence.

For the first time during the hearing an emotional Mr Hayes also expressed remorse about what had happened under his watch.

“I knew every child in my school. I knew 90 per cent of the parents by first name and so that catastrophic situation that happened, all that happened in the last six years has been central to me, but I’ve never forgotten where the real pain lies.”

A short time later Commissioner Jennifer Coate excused Mr Hayes, before his superior Christopher Fry took the stand briefly.

The hearing continues on Thursday.