Every major Australian church has been cautioned to better protect children or risk illegitimacy.

In a speech to the National Council of Churches, the Royal Commission into Institutional Responses to Child Sexual Abuse chairman Justice Peter McClellan urged religious leaders to act on his recommendations.

"What we can be certain of is that any institution which does not acknowledge past wrongs and the need for change will lose the confidence of Australians," he said via a recorded video.

"The community will not accept the legitimacy of any institution which does not give priority to the safety and wellbeing of the children for which it has responsibility."

Justice McClellan detailed the exhaustive work of Australia's largest royal commission, which has examined 1.2 million documents and heard evidence from more than 1,200 witnesses over 440 sitting days.

What is a royal commission? The highest form of public inquiry commissioned by the Australian Government into matters of great national importance

The highest form of public inquiry commissioned by the Australian Government into matters of great national importance Set up temporarily on an ad hoc basis, royal commissions draw on public input and can take place over several months or years

Set up temporarily on an ad hoc basis, royal commissions draw on public input and can take place over several months or years They have wide-ranging powers to cross-examine, obtain evidence, and protect witnesses

Fifty-nine per cent of abuse reported to the royal commission has come from within religious institutions.

Justice McClellan revealed the commission had referred 2,025 cases to police and other authorities but only 127 have been acted upon.

"The volume of referrals is so great it will take some time before all the matters are processed and prosecutions commenced," Justice McClellan said.

The chairman detailed the necessity for a national redress scheme, outlining the Australian Government's preferred "opt-in" system for payment to survivors.

"The commissioners understand that many churches and religious groups have indicated that they are positively disposed to the Commonwealth's scheme," Justice McClellan said.

"This is very pleasing to hear."

The royal commission has released dozens of public issues papers and recommendations over the past two years.

Mandatory national reporting laws still being considered

Justice McClellan stressed to the National Council of Churches the need for reporting abuse.

"Failure to report abuse to the authorities may leave a child, or perhaps a number of children, exposed to abuse," Justice McClellan explained.

"Reporting offences may be particularly important in an institutional context. Institutions may be conflicted.

"Imposing criminal liability for failure to report is likely to encourage reporting despite the damage this may inflict on the institution's reputation."

NSW and Victoria already have laws against concealing child sex crimes.

"The royal commission is considering whether it should recommend that other states and territories follow the lead of New South Wales and Victoria, and if so, what might be the appropriate terms of that offence," Justice McClellan said.

Although initially uncertain, Justice McClellan is now convinced the royal commission will make Australian children safer.

"I am often asked by people whether I believe that much will change as a result of the royal commission," he told church leaders.

"Although in the early days of the royal commission the question could not be answered, I am now able to confidently give a positive answer.

"Although there may be some people in some institutions who resent the intrusion by the royal commission into their institution, the overwhelming response is positive."

The commission is moving towards completing its work in December, and Justice McClellan said he wanted to ensure all institutions remained included in the conversation.

"I have previously said that the royal commission's work has changed the conversation about child sexual abuse in Australia," he said.

"Institutions must make the changes necessary to ensure, as far as may be possible, children are not abused in the future."