The Jehovah's Witnesses will continue adhering to a 2000-year-old rule in handling child sex abuse cases or cruelly shunning victims who leave the organisation "because the Bible says so", an inquiry has heard.

Challenging the church's stance, child sex abuse royal commission chair Justice Peter McClellan said on Friday that other parts of society did not shun victims like the Jehovah's Witnesses do if a survivor disassociates from the organisation "for their own survival effectively".

"It's a pretty cruel way of dealing with someone who has suffered sexual abuse," he told two senior Australian members of the restorationist denomination.

"To take away, by reason of the rules that you impose, all of their social structure, it's cruel."

Counsel assisting the commission Angus Stewart SC says the organisation has failed to address the particularly devastating practice of shunning survivors who disassociate from the organisation because of their abuse.

Jehovah's Witness Australian branch committee member Terrence O'Brien said disassociation was an individual's choice.

"They are actually taking the stand to shun the congregation. They understand the implications of that," Mr O'Brien said.

"I agree it puts them in a difficult situation but it is a choice."

Rodney Spinks, who advises Australian church elders on how to handle child sexual abuse cases, said victims of child sex abuse are not shunned.

Justice McClellan questioned why shunning was necessary, leading Mr Stewart to tell the two witnesses: "The real answer to the question is because you say the Bible says so."

Mr O'Brien agreed it was the organisation's understanding of the scriptural doctrine.

He confirmed the Jehovah's Witnesses' two-witness rule that applies in all cases of complaints of wrongdoing will remain because it is required by scripture and cannot be changed.

The commission found the organisation wrongly relied on that rule in the context of child sexual abuse, saying complainants were subject to ongoing traumatisation if their allegation was not corroborated by a confession by their abuser or a second 'credible' eyewitness.

It found the Jehovah's Witnesses did not adequately protect children from the risk of being abused.

But the senior church members dispute its finding that the organisation has a general practice of not reporting child sexual abuse allegations to police or authorities unless required to do so by law.

"We have never had a practice of not reporting," Mr O'Brien said.

The inquiry has previously found the Jehovah's Witnesses did not report a single one of 1006 alleged perpetrators identified in their own case files since 1950. Commission staff have now referred 514 of those to the police.

Mr O'Brien said hundreds were reported, although not by the organisation because it was left to the elders handling the case or the parents.