But Professor Parkinson has told Lateline he has withdrawn his support for the protocol because the church failed to take action over clergy who do not comply.
He alleges a church cover-up as late as 2005 put children at risk.
And he says the church behaviour alleged by New South Wales Detective Chief Inspector Peter Fox and Victorian police amounts to "organised criminality".
Responding to the announcement of a royal commission into institutionalised child sexual abuse, Cardinal Pell drew on the authority of Professor Parkinson.
"We follow the Towards Healing procedures here in Sydney. They were set in place in early 1997. They have been twice reviewed by Professor Parkinson, one of the leading authorities in the area," Cardinal Pell said.
"Since 1997 one of the significant protocols that's in place is, [it's] completely prohibited to shift priests who have been charged, to shift them around. If and where that has been done, that is against the protocols."
Professor Parkinson was involved in regularly reviewing the Towards Healing protocol up until 2009.
He says he no longer supports the document, or the church body that it established to investigate any failures.
"My disagreement with the Catholic Church has been that I have challenged them over failures to comply with the letter and spirit of the protocols," he said. "As a matter of integrity I could no longer support the National Committee of Professional Standards while there was a gap between their rhetoric and their actions."
Priests 'moved overseas'
Professor Parkinson is very disturbed by the fact that three separate allegations of serious child sexual assault were made against three different priests in an order known as the Salesians.He is concerned the church allowed the accused men to travel overseas when they were under investigation by police, and says they were not brought back to Australia to face their accusers.
"They are one of the largest ministries in the world," he told Lateline. "There were three cases in which priests had been moved overseas or kept overseas. It concerned me very deeply and I told them they needed to have a public inquiry into this, but eventually the national committee suppressed the report that I eventually [gave] on those cases."
Professor Parkinson also gave this evidence to the Victorian inquiry into child sexual abuse.
The Catholic Church maintains that a vast bulk of cases of child sex abuse are historic, but Professor Parkinson says the alleged cover-up involving the Salesians happened in the past decade.
"These events all occurred after 1996 and that was the point I made, this was not just historical," he said. "It was things that occurred between 1998 to 2005. I think the suppression of my report was also a cover-up and that brings us to the present day."
Professor Parkinson says one of the priests was a convicted sex offender who was sent to Samoa, and he appears to have had contact with children.
"[I am] very angry and very concerned - I cannot tell all of that story on air," he said. "These are serious issues and when Samoan children were put at risk, and I feel they were, we ought to hold their heads in shame. I was calling the church to account, because they asked me to review Towards Healing. As a matter of integrity I had to confront them with that. Their failure to take responsibility and the failure to deal with those issues made me angry, indeed and it still does."
Call for independent inquiry
Professor Parkinson made several attempts to get the Catholic Church to take action against the Salesians.He called for the church to instigate an independent inquiry and in February 2011, he met with a senior church official, Father Brian Lucas.
Professor Parkinson said in his submission to the Victorian clergy abuse inquiry:
"Father Lucas indicated to me his strong opposition to having an independent inquiry. He said it would be embarrassing for the Salesians and very expensive."Father Lucas told Professor Parkinson a copy of his report would be placed on the church's website.
But the professor told the inquiry:
"The version prepared by Father Lucas was only two pages long and I regarded it as totally inadequate."In June 2011, Professor Parkinson wrote to the co-chair of the National Committee for Professional Standards, which investigates complaints against clergy, Archbishop of Adelaide Philip Wilson.
He asked Archbishop Wilson to set-up a judicial inquiry into the matter with the Victorian Government.
Professor Parkinson told the inquiry Archbishop Wilson never responded officially to his letter.
He says the church suppressed his report for more than a year until he released it to the Victorian inquiry.
"Finally after waiting 14 months for the church to release that report I went public in 2011 and said that the church suppressed my report, and with the Victorian inquiry there was an opportunity to make it available to the Parliament of Australia," he told Lateline.
Under parliamentary privilege at the Victorian inquiry, Professor Parkinson said:
"The cover-up of these matters continues to the present and people at the highest levels of the Catholic Church nationally have been involved in that cover-up."Professor Parkinson has welcomed the royal commission into institutional responses to child sexual abuse and says the issues of celibacy, secrecy and Catholic culture must be scrutinised.
He says many of the allegations against the church are tantamount to organised crime.
"But very serious allegations have been made by the Victorian police inquiry and by DCI Fox," he said.
"[They] are of immense seriousness and a royal commission must get to the bottom of this and must look at what are essentially allegations of organised criminality."
The NSW Department of Public Prosecutions is now looking at whether Archbishop Wilson and Father Lucas were involved in the alleged cover-up of child sexual abuse by another priest, Father Denis McAlinden.
The Federal Government will announce the terms of reference for the royal commission before the end of the year.
Statement from the Archdiocese of Sydney
Katrina Lee, the director of Catholic Communications at the Archdiocese of Sydney, provided this response to Lateline:Cardinal Pell met Professor Parkinson in recent months, and Professor Parkinson did not raise any concerns with him about the Archdiocese of Sydney's compliance with Towards Healing and the criminal law.
The Catholic community is grateful for the important work Professor Parkinson has done in reviewing and strengthening the Towards Healing procedures since they were established in 1996.
He has clearly shown that the Salesian order has some important questions to answer. If he is aware of any evidence of criminal non-compliance he needs to take it to the police.
Professor Parkinson's estimates about the incidence of abuse by Catholic clergy need to be examined and tested, and the Royal Commission will provide an opportunity for this.
Professor Parkinson's estimates are significantly at variance with US data, including a 2003 US review by Professor Thomas G. Plante of the University Santa Clara, which found that approximately 2 per cent of Catholic clergy had abused children, and that Catholic clergy are no more likely to offend against children than other clergy, members of professions in close contact with children, or adult males in the general population (cited in Fabien M. Saleh et al, Sex Offenders: Identification, Risk Assessment, Treatment and Legal Issues, Oxford University Press 2009).
In his evidence before the Victorian Parliamentary inquiry, Professor Parkinson said: "It is important to emphasise that all churches now, including the Catholic Church, are very much safer places than they were. We have, in my view, come a long way, but there is a long way to go." Cardinal Pell made a similar point yesterday.