In a report released on Monday,the commissioners found that Mr Houston and the church's executive team failed the victim,known as AHA,who was molested by Frank Houston for a number of years from the age of seven.
When the allegations surfaced almost 30 years later in 1999,Mr Houston confronted his father,who admitted abusing AHA.
The commissioners found that Brian Houston,then national president of the Assemblies of God in Australia,did not inform authorities.
"We are satisfied that,in 1999 and 2000,Pastor Brian Houston and the National Executive of the Assemblies of God in Australia did not refer the allegations of child sexual abuse against Mr Frank Houston to the police,"the commissioners wrote in their report.
The commission heard that Mr Houston suspended his father from the church but it was decided at a meeting of senior Assemblies of God members the allegation would be kept confidential and Frank Houston would be allowed to quietly retire without the reason being made public.
"We consider that a conflict of interest first arose when Pastor Brian Houston decided to respond to the allegations by confronting his father while simultaneously maintaining his roles as National President (of the Assemblies of God in Australia) and Senior Pastor,"the commissioners found.
The report concluded that senior staff at the Assemblies of God failed to follow their own protocol regarding sexual abuse claims and did not support the victim.