A statement was given to Australia's royal commission into institutional responses to child sexual abuse carried out by the high-profile leader.
It is examining the reaction to the scandal surrounding Frank Houston, a preacher who was heavily involved in Australia's Pentecostal movement.
He is now dead and had admitted to sexually abusing a boy in New Zealand.
He made the confession in 2000 and was immediately dismissed by his son, who was then national president of the Assemblies of God.
In the statement, Brian Houston explained how, while there had been no allegations against him or Hillsong, the scandal had affected him "in a very personal way".
"Having to face the fact that my father engaged in such repulsive acts was – and still is – agonising," he said.
He added: "However, as painful as this is for me, I can only imagine how much more pain these events caused to the victims, and my prayer is that they find peace and wholeness.
"Hillsong Church has zero tolerance for sexual abuse and has comprehensive child protection policies that are continually reviewed. We also welcome any recommendation of the commission that would assist us to improve on these policies even further."
The commission is also examining allegations against two other men.