A former Pentecostal pastor at a Sunshine Coast church cannot accept that a former youth leader who married his daughter is a paedophile, an inquiry has heard.

Jonathan Baldwin was jailed for a maximum of eight years in 2009 for molesting a 13-year-old boy for two years at the Queensland church.

The church, which could not be named for legal reasons, was attended by about 200 people.

Baldwin had a non-parole period of four years and was no longer in jail.

His father-in-law and former boss, Ian Lehmann, told the Royal Commission into the Institutional Responses to Child Sexual Abuse on Wednesday that Baldwin made an error in judgment but was not a paedophile.

"I have two grandsons by him. A third one about to be born," he said.

"If I believe he is a paedophile, then I've got to accept the reality that our three grandsons are at great risk."

'I don't think I'm sharing wine with a paedophile'

Peter O'Brien, the lawyer representing ALA and his family asked how he could believe his son-in-law was not a paedophile when he had been convicted and jailed for child sexual abuse.

"So even today when you give evidence at this royal commission on oath, you do not accept that your son-in-law is a paedophile, not withstanding his convictions and his subsequent unsuccessful appeals?"

But Mr Lehmann continued to state that he did not believe Baldwin was a paedophile.

"No, I would not view him that way, I have to say that," he said.

"When I sit down and have a meal with him, share a bottle of red wine with him, I don't think I'm doing this with a paedophile."

Mr Lehmann told the commission he did not believe Baldwin's behaviour was deviant, despite being approached by church staff on three occasions with concerns about Baldwin's relationship with ALA.

ALA's father said the church failed in its duty of care to a victim who was "broken" after Baldwin was found guilty and jailed for the offences, including one count of "maintaining", eight counts of indecent treatment of a child under 16 and one count of sodomy.

Earlier on Wednesday ALA's father told the inquiry the church involved "wiped their hands" of his son.

In a statement to the inquiry, the man said his son was abused by Baldwin in Queensland from 2004 to 2006.

The commission's current hearings is looking at what support was provided to the family during the criminal process and how the offending pastor was removed.

The father told the royal commission the abuse began when his son was 13 years old.

The man said that in 2010 his son launched civil proceedings against the church for negligence "because he felt that he was entitled to justice and compensation as a result of his abuse and because the church had not been forthcoming".

The civil matter was settled out of court in 2012.

"Our concerns were that the church from where the abuse originated wiped their hands of [my son] even after the trial confirmed the man's guilt," the father said.

"They should have come back to him with support."

Son 'dragged through the courts'

He said not only was his son abused by a church leader but the church mistreated him when he reported it.

"From the ages of 12 through to 21 our son was first sexually abused by a church leader, then when he called for help he was shunned, dragged through the courts," he said.

"His church shattered his teen years. Then he was left with a massive legal bill to boot.

"How much abuse and kicking should a victim of church negligence have to take?"

He said the church put its leaders, money and assets above victims.

"The church clearly prioritises so-called important people, money and assets far above victims of abuse under their watch," he said.

"The imperative of running a profitable business far surpasses any concern for the pain of anybody hurt along the way."

Victim too traumatised to appear at royal commission

The man cried as he read a statement from his son, known as ALA to the royal commission, who he said was afraid to appear because of feelings the inquiry may stir up, and because the pain haunts him every day.

"Would Jesus molest a child? Clearly the answer is no," the statement said.

"If the child was molested would Jesus protect that child from further abuse? Obviously yes. Would he expose the perpetrator? Yes. Would Jesus allow the abuse to continue? No.

"Then why does the church, those who claim to represent Jesus, do the exact opposite? Are they really demonstrating the character and nature of God, or something else?"

In the statement ALA added: "It's now time for real, open and honest change. It's time to look after the victims if in fact it isn't already too late."