Mr Ellis, who has first-hand experience of Towards Healing, said the main problem with it and the parallel Melbourne Response was an inherent conflict of interest: cases are managed by church-appointed personnel, although complainants are encouraged to go to police.
The policies will be discussed at an Australian Catholic Bishops' Conference meeting in Sydney starting on Monday.
"I think ultimately they are probably going to have to start again," Mr Ellis said of Towards Healing, introduced in 1997.
Some victims struggled with "a perception and a reality of coming to the body that has been responsible for causing harm to you and asking them to do something about it".
"I can understand the theory of (Towards Healing) and why the Catholic bishops' conference in the mid 1990s thought that was a good thing and they should be doing that, but when you look at that objectively and when you talk to victims and survivors about it, that's a fundamental problem."
Mr Ellis was sexually abused in the 1970s, starting when he was a 14-year-old altar boy in a western Sydney parish.
The perpetrator, a priest, is dead.
Mr Ellis built a successful career in law but suffered a breakdown in his late 30s as his experiences came back to haunt him. He tried Towards Healing, found it wanting, then sued the Sydney archdiocese trustees and lost when the NSW Court of Appeal ruled they could not be held liable for damages over abuse claims.
Although costs of more than $750,000 were awarded against him, Mr Ellis asked the church to formally agree to waive them, which it did 20 months later.
Since then the church has funded some hundreds of thousands of dollars worth of his counselling and other expenses: the exact figure is disputed and the subject of negotiations.
Mr Ellis estimates lost earnings of $3.5 million to $4m because of the abuse and its consequences, including the legal battle.
He has also paid for counselling and support of other victims. He has built a new legal career, handling about 60 claims against the church and other institutions, mostly over sexual abuse.
He said even if the conflict of interest victims identify in Towards Healing could be worked around, the management of people seeking redress is inconsistent, and at its worst is neither transparent nor accountable.
Professor of Intercultural Studies at RMIT University Des Cahill said Towards Healing and the Melbourne Response were primarily designed to protect the church's reputation and financial assets.
"They were being pressured by the Vatican to apply canon law to the issues rather than Australian criminal law, and Catholic canon law protects the rights of the priests but has nothing to say about the children and their rights," Professor Cahill said.
He proposes the bishops at next week's meeting consider setting up an expert committee, including experts in victimology, to develop and implement "a multifaceted strategy of healing and reparation involving the whole Australian church".
President of the support group Broken Rites, Chris MacIsaac, said an independent body should manage complaints.
"Broken Rites wants a more transparent process, conducted by an independent authority, to examine claims and determine remedies appropriate to comparable civil personal-injury claims," Ms MacIsaac said.
"Too often, victims felt re-abused by Towards Healing."