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.
The Vatican and one of Australia's top clerics had failed to properly deal with child sex abuse victims, a retired bishop has said.