Hillsong founder Brian Houston gave sermons at the church alluding to "a serious moral accusation" against his father without explicitly stating he had sexually abused a child.
Frank Houston admitted abusing a young boy at a home in Sydney's Coogee in 1970, which he confessed to his son in 1999.
Houston is charged with concealing the crime until his father's death in 2004, to which he pleaded not guilty.
Further allegations of abuse also later came to light leading Houston to this week brand his father a "serial pedophile".
Under cross-examination on Wednesday, Houston was grilled about the contents of a sermon he gave to hundreds of worshippers at the Hillsong Church Hills Campus in 2002.
Crown prosecutor Gareth Harrison put to Houston he had "sanitised" his father's deeds to protect the church from scandal, which he denied.
"When you started to make announcements to your congregation ... you didn't talk about sexual abuse of a child by your father ... you were more subtle," Mr Harrison said.
"You alluded to things that he had done wrong, but you didn't hit the nail on the head."
"It's true that I didn't talk about the specifics of exactly what Frank had done to the whole congregation," Houston said.
Houston told the congregation he had confronted his father about the accusations which led to "certain confessions" about "issues", according to a transcript of the sermon read in part to Sydney's Downing Centre Local Court.
"You haven't said what the confessions were. You haven't even said what the issues are," Mr Harrison said.
Houston also said during the sermon: "My dad, he loves God. He still loves God. He's still in the word."
Mr Harrison suggested "what you were really saying was 'despite this part of his life that got out of hand, he's still a good man'."
Houston said it was "not necessarily" his intention of conveying that to the congregation.
Mr Harrison put to Houston he chose the words of the sermon carefully to "disguise the truth", which he denied.
"You're trying to fool them into thinking this was a serious allegation, but not an allegation about child sexual assault."
"I never tried to fool the congregation," Houston said.
Following his father's confession, Houston informed a meeting of the church's national executive who banned Frank Houston from preaching. However, Houston told the court this week he did not go to police as it was not the victim's wish to do so.
Earlier this week, Houston told the court how difficult it was for him to talk about his father's crimes and how he struggled for years to use the word "pedophile" to describe him.
"I found it tremendously difficult every time I had to tell the story again," Houston explained.
The hearing continues
