In his final day of evidence, the evangelical preacher told the Royal Commission into Institutional Responses to Child Sexual Abuse of learning the extent of his father's alleged predatory acts in the 1960s and 1970s.

He told the commission he first became aware of allegations of abuse in 1999 but learned in 2000 there were further claims involving six boys in New Zealand.

When asked by counsel assisting, Simeon Beckett, whether he accepted that Frank Houston had abused other children, Brian Houston responded: "We probably don't know how many. We may never know how far it went."

Frank Houston, founder of the City Christian Life Centre which merged with the Hills Christian Life Centre to become Hillsong Church, died in 2004 without being charged with any offence.

Brian Houston defended the way he responded to the child abuse allegations against his father and denied that he deliberately tried to conceal his involvement in a $10,000 compensation payment to one alleged victim, given the pseudonym AHA.

In his statement tendered to the royal commission, Brian Houston said he believed two payments had been made to the alleged victim by his father.

However, in evidence he recalled a conversation with AHA, in which AHA said he had not received a $10,000 payment that had been promised at a meeting with Frank Houston at a McDonalds in Thornleigh.

"He was very frustrated," he said. "He hadn't received the compensation. We had let AHA down."

Brian Houston said he arranged for an unnamed family member to ensure the payment was made.

Under cross-examination by AHA's counsel, Karen McGlinchey, he admitted he sought advice from prominent law firm King & Wood Mallesons regarding the allegations against his father.

Brian Houston was the head of the Pentecostal church umbrella organisation Assemblies of God when the claims surfaced, but denied he had a conflict of interest in handling proceedings against his father.

"The whole idea of a conflict of interest never occurred to me," he said. "I saw it as me being in a role having to make tough decisions and having the guts and the courage to make those decisions."

However, he admitted he took too long to respond to whistleblower pastor Barbara Taylor, who first brought the allegations to light, blaming "stress, busyness and trying to keep above my own emotions, which were not in good shape."

The public hearing is examining the response of Australian Christian Churches and affiliated Pentecostal churches to allegations of child sexual abuse.

Hillsong Church, Northside Christian College - now known as Encompass Church - and a Pentecostal church on the Sunshine Coast are included in the inquiry.

The hearing, before Justice Jennifer Coate, is expected to continue until October 17.