Hillsong Church leader Brian Houston has told an inquiry he did not report child sexual abuse claims against his father to police because the victim was over 18 when he came forward.

The Royal Commission into Institutional Responses to Child Sexual Abuse is examining the handling of allegations against William Francis Houston, better known as Frank.

Brian Houston said he was told in October 1999 that a man in his mid 30s, known as AHA, had come forward to reveal that Frank Houston had abused him about 30 years earlier.

He told the inquiry he was in no doubt that a criminal offence had been committed.

"Rightly or wrongly I genuinely believed that I would be pre-empting the victim if I were just to call the police," he said.

"If he decides to go to the police he can, or if anyone else decides to go to the police they can.

"If this complaint was about someone who was under 18 then and there, I am absolutely certain we would have reported it to the police.

"We would have made sure that's where it went."

Brian Houston 'devastated' by sex abuse claims

Brian Houston said he would never forget the day he was told about his father.

"(I) cried, went home," he said.

"I was devastated, to be honest with you, totally devastated."

Brian Houston said in hindsight he believed his father knew what was coming in mid-1999 when he suddenly decided to retire as head of Sydney Christian Life Centre .

The church was later merged into the Hillsong church.

"I believe he knew that issues were coming to a head," he said.

"The way I look at it now he was a desperate man treading water."

Evidence before the commission revealed that Frank Houston had been approached by members of one church in February 1999 on behalf of the victim known as AHA.

The churches were all affiliated to the Assemblies of God and Brian Houston was the president.

However, it took eight months before Brian Houston was told about the allegations against his father.

Earlier on Thursday an executive of the Assemblies of God churches admitted breaching church procedure when hearing about allegations against Frank Houston.

Former national secretary Keith Ainge told the inquiry he agreed to invite Houston to join a rehabilitation program in 1999.

Mr Ainge said the church had a rule of never rehabilitating a paedophile, but the decision was made under pressure.

"Frank Houston was a well-known, respected and appreciated member of the Assemblies of God, and everyone was totally shocked and devastated," he said.

Remorse at allowing son to deal with father

Pastor Ainge also said he failed to recognise the conflict of interest in allowing Frank Houston's son, Brian Houston, to deal with the complaint against his father.

The commission heard on Wednesday that Brian Houston raised allegations against his father at a national executive meeting in December 1999.

Mr Ainge said Mr Houston told the meeting his father was accused of sexually immoral behaviour towards a minor.

The meeting moved immediately to suspend Frank Houston but did not recommend the matter be referred to police.

Brian Houston told the commission on Thursday he did not believe he had a conflict of interest in dealing with the matter.

"Internally, definitely I was conflicted, if you are talking about coming to grips emotionally with what my father did," he said.

"But if you are talking about defending my father, what he did was undefendable (sic).

"I don't feel that that was a consideration at all."

The inquiry continues.