Frank Houston also told his son that his own grandfather had come home drunk one night and abused him when he was growing up, the court was told on Monday.
Brian Houston, 68, is accused of covering up his father's abuse until his death in November 2004, after he confessed the crime to him in 1999.
Houston has pleaded not guilty and told the court his father had met his victim at Sydney's Redfern station and organised to pay him $2000, later topped up with a $10,000 payment when Houston intervened.
"It was his feeble attempt to try and right the wrong," Houston said on Monday.
The founder of Hillsong mega church also said he spoke to his father's victim on the phone and offered him counselling on behalf of the Assemblies of God in Australia (AOG).
"He said 'I don't want your bloody counselling' and he cut the meeting short," Houston said.
Houston told the court he was involved in organising to pay the victim an additional $10,000 which he did through a lawyer to avoid it appearing like a cover-up.
He told the court he wanted to make sure that in paying the money he was not in any way silencing the victim or preventing him from going to the police in the future.
"I was wanting to be careful that there was no cover-up here ... and it couldn't be seen that there was a cover-up," Houston told the court.
He also said it was his intention to distance himself and the church from the payment.
"I wanted to be sure whatever document was being drawn up that this was a payment from Frank to (the victim) - between those too," Houston said.
"I was trying to stay arms length from it."
Houston said he later received a call from the victim saying he had not been paid and had been told by Frank Houston that he had no money.
"I was frustrated that no money had been paid but also I was frustrated Frank had told the victim to phone me," Houston said.
Houston said it was his understanding the money was eventually paid but he did not know by whom.
"Do you know what the terms for the payment ended up being?" Houston's lawyer Phillip Boulten SC asked him.
"No," he replied.
Houston told the court his father claimed the abuse was a one-off, despite other allegations later coming to light.
""He told me it was a once off incident, done at a time when he was emotionally low," Houston said.
He described his father at the time of dealing with the fallout from the abuse as "embarrassed, ashamed, humiliated, deflective, depressed".
Houston also recounted informing a room full of around 35 church pastors about his father's abuse in around 2000 when it came to light.
"I found it tremendously difficult every time I had to tell the story again," he told the court.
The hearing continues in Downing Centre Local Court
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