The founder of Hillsong Church, Brian Houston, failed to report allegations his father had sexually abused children and had a conflict of interest in dealing with the accusations, a royal commission has found.

Frank Houston abused up to nine boys in Australia and New Zealand and in October 2014 a royal commission was launched into the institutional responses to abuse, the Guardian reports. The commission investigated the Assemblies of God Australia (now Australian Christian Churches) and found several failures within the church executive which at the time was led by Frank Houston's son, Brian. Hillsong Church, of which Brian is now the pastor, had not been founded at the time of the abuse.

The royal commission found that neither the Church's national executive nor Brian Houston referred the allegations to the police.

Additionally Houston "had a conflict of interest in assuming responsibility for dealing with AHA's [the victim's] allegations because he was both the National President of the Assemblies of God in Australia and the son of Mr Frank Houston, the alleged perpetrator," the commission ruled.

When the abuse was reported decades after it had occurred, Brian confronted his father who confessed. He then called a meeting of the national executive and resigned as chair but remained present during the discussions surrounding the allegations and subsequent disciplinary actions.

The victim, referred to as AHA, told the commission he had been sexually abused by Frank Houston as a seven and eight year old boy in 1969 and 1970. The former preacher, who died in 2004, would stay with AHA's family on Sydney visits and come into his room "nearly every night of the week" to abuse him.

AHA also alleged Frank Houston abused him when they were alone in Houston's office on an evangelical camp.

"The abuse in my home and at the different church meetings continued over a period of years until I reached puberty," AHA told the commission. "Pastor Frank wanted nothing to do with me after I reached puberty."

The victim told his mother eight years later in 1978 but was warned off reporting it as the Houstons "were almost like royalty" in church circles. Eventually his mother brought the allegations to the church decades later in 1999.

After Frank Houston confessed to his son Brian, the assemblies of God executive began investigations and discovered a further eight alleged victims. However none of them were made public and Brian Houston wrote to the churches saying there was "no reason" for it be announced.

He defended his decision not to go to the police and told the commission his father was stood down instantly.

Statements from both Houston and Hillsong sought to distance the church from the allegations with Houston pointing out the abuse claims happened before Hillsong existed.

"The royal commission did not directly involve Hillsong church," the church board and elders said in a statement released today. The abuse by Frank Houston "occurred many years before Hillsong Church existed."

The statement said it supported the objectives of the royal commission but also supported Brian Houston's conduct saying it was "easy to look back many years in hindsight."

"Pastor Brian acted in the best way he felt at the time and took decisive and immediate action against his own father," read the statement. "We are confident that the actions of Pastor Brian, from the moment he discovered the news about his father, were done with the best intentions towards the victim.

"The findings of the royal commission confirmed that his actions resulted in the perpetrator being immediately removed from ministry."