Bishop Geoffrey Robinson told a national inquiry the Church had failed to speak out strongly about the abuse.
The bishop played an important role in developing the Australian church's response to the issue in the 1990s.
Australia is holding a national inquiry into institutional responses to child sexual abuse.
Popes and archbishops, including the Vatican's finance chief, Australian Cardinal George Pell, had sent out the "wrong message" about the issue, Bishop Robinson told the inquiry on Monday.
"I think that some popes gave out the wrong message ... and some archbishops too," local media reported Bishop Robinson telling the Royal Commission into Institutional Responses to Child Sexual Abuse.
Bishop Robinson said Pope John Paul II did not immediately condemn the abuse claims when they emerged in the 1990s.
"We still haven't had that kind of leadership, not even from (Pope) Francis," he said, explaining that bishops followed the Vatican's line by remaining silent on the issues.
Bishop Robinson said that while he was drafting a national response for the Australian Catholic Church to abuse victims in 1990s, the then Archbishop of Melbourne, Cardinal Pell, released his own protocol for Melbourne.
Unlike the national strategy, it required alleged sex abuse victims to speak to church lawyers first.
"(Pell) would later claim that this meant he was the first person in Australia to have such a protocol," said Bishop Robinson.
"He destroyed our unity," he told the Commission.
More than 4,000 victims have come forward to the Royal Commission, which is looking at how religious groups, charities and state care providers responded to child sex abuse allegations.

Landlords who let properties to more than three unrelated people need to apply for a licence for a House of Multiple Occupation (HMO).
But many are put off - because a licence can cost ??1,000 - despite facing a fine of up to ??20,000, Southampton City Council said.
The authority estimated a total of 1,500 unlicensed HMOs in the area.
Shelter helpline adviser Nadeem Khan said fear of eviction and living in poorly maintained properties are frequent concerns raised by HMO tenants.
"Because of the huge shortage of affordable homes people are being forced into rented homes which are unregulated. We receive about five or six calls a day about this," he said.
Nationally, mandatory licensing for HMOs is aimed at houses of three storeys or more and occupied by five or more unrelated people.
In Southampton, the licences affect properties in Bargate, Bevois, Portswood, Swaythling (Designation 1 - introduced in 2013) and in Shirley Freemantle, Millbrook, and Bassett (Designation 2 - introduced in 2015).
A council spokesman said: "Landlords have generally co-operated with the regime, but a small minority have resisted applying for their licence."
The council said it had so far gained prosecutions against one firm and 13 individuals.

The incident happened in Forbes Road at about 10:25. The van driver had picked up the thief in Yeaman Place in his red Renault Trafic van.
As he dropped him off in Forbes Road, the thief pulled out a knife.
He took a two-figure sum of money and left in the direction of Bruntsfield Place.
He was about 30 years old, white, about 6ft tall and of medium build. He was wearing a dark jacket with a white stripe on the sleeve and dark jeans.
Police have appealed for witnesses.
Det Con Joyce Gunderson said: "Thankfully the van driver was not injured during this robbery but he was left understandably shaken.
"We are pursuing various lines of inquiry to trace the man responsible and we are keen to hear from anyone who can assist us in identifying him.
The Vatican and one of Australia's top clerics had failed to properly deal with child sex abuse victims, a retired bishop has said.
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Tenants in Southampton may face eviction because landlords are holding incorrect paperwork, Shelter claims.
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A thief who stole money at knifepoint from a van driver he had just caught a lift from in Edinburgh is being sought by police.