On Friday, the committee revealed it had asked the church to hand over those documents.
Church spokesman Father Shane Mackinlay says it will cooperate with the inquiry.
"We have no reason to withhold any of those sort of files," he said.
"They've asked for access to files and to the extent that that's something they want to see, we have no concern about that."
Earlier, the inquiry heard shocking claims that decades ago, two boys had died at the hands of paedophiles at orphanages run by a Catholic order in Melbourne.
Dr Wayne Chamley, a researcher with the child protection group Broken Rites, made the startling allegations against the Hospitaller Order of St John of God, which ran orphanages in Melbourne's outer east from the 1960s to the 1980s.
Dr Chamley said there was a group of religious brothers who abused boys under the leadership of what he called an "alpha paedophile".
"This crowd, they would stop at nothing to get access to children and to do anything to cover it up," he said.
Dr Chamley alleges the crimes that took place at those orphanages go beyond sexual abuse.
He believes two boys died while in the care of the order.
"Three residents independently told me about this boy who was attacked by a pack of four and eventually thrown down a staircase and was taken to the infirmary and was never seen again," he said.
"Now what happened, we will never know, but if you had children who had no family, the family wouldn't even know that the person was deceased."
He also told of boys being locked up in institutions because they tried to escape.
In a written statement, St John of God said it became aware there had been sexual abuse in its Victorian facilities in 1997.
It said the order investigated and reported the abuse to police and ultimately there was a multi-million-dollar mediated settlement.
Not brought to justice
Patrick Tidmarsh is a forensic interview adviser with Victoria Police with decades of experience interviewing child abuse victims and perpetrators.
On Friday, he told the inquiry clergy he had dealt with were not brought to justice.
"I wracked my brains," he said. "I could not think of a single case where they were not known, had not been moved, had re-offended and in most cases several times after that moved again and re-offended, moved again and re-offended."
Mr Tidmarsh said one of the most important requirements for investigators was to have an open mind.
And he said the church did not have the independence, the expertise nor the motivation to investigate properly.
"I don't think they should be investigating themselves," he said. "I think that is absolutely the number one issue. I find it extraordinary that an organisation has set up a separate system, particularly one where if you volunteer for that system you give up your rights to any other system."
Wrapping up his evidence on Friday afternoon, Dr Chamley told the inquiry most offenders go on to lead very comfortable lives with the support and protection of the church.
"Compare it with say many of the victims that we see; 60 per cent of them I believe have got post-traumatic stress disorder," he said. "I'd say 90 per cent have entrenched psychiatric illness."
Dr Chamley said many of the victims were worried about what would happen to them in their dotage.
"The memory that lasts is your childhood memory; what a memory to be stalking them for the remaining 10 or 15 years of their life," he said. "Maybe they'll go into an aged care home re-institutionalised again. This is what they all talk to me about; the fear of what is going to happen to them. The Catholic Church just doesn't seem to have any idea what these people are facing and I just can't understand it."