In a Christmas message, the Australian church's most senior cleric said he was "deeply sorry" for the hurt that had occurred, describing it as "completely contrary" to Christ's teachings.
But he stopped short of specifically mentioning allegations of child abuse by members of the clergy.
"I feel too the shock and shame across the community at these revelations of wrongdoing and crimes," Cardinal Pell said.
His apology came after the federal government this year announced a royal commission to the response of institutions, including the church, to cases of child abuse in Australia.
Bravehearts founder Hetty Johnston said Cardinal Pell's statement represented a "cultural shift" in the church as it comes to terms with the role played by some its clergy.
Not all victims would find solace in his words, but it was an important message that needed to be said, she added.
"The silence, secrecy and the shame which the church have been leaders in, are the offenders best friend and our children's worst enemy," Johnston said on Monday.
"I think they're finally ready to face the demons and face the past and to hopefully put it behind them."
Catholics who had deserted the church over its handling of child abuse might also find some comfort in knowing Cardinal Pell had acknowledged the suffering, she said.
A spokesman for victim support group Broken Rites, Wayne Chamley, said the church was beginning to "appreciate" the scale of its involvement in child abuse since the royal commission was announced.
"It's pleasing that he's opening up his heart to these people," Chamley told ABC television.
"I don't think we've seen a statement in the past which was reflecting on the scale of what's gone on."
The church has been accused of covering up its involvement in child abuse by silencing victims, hindering police and alerting offenders.
One senior New South Wales police investigator's damning testimony into how the church destroyed evidence and moved accused priests around the country prompted Prime Minister Julia Gillard to announce the royal commission in November.
In his statement, Cardinal Pell said people had "suffered at the hands" of fellow Christians, Christian officials, priests and religious teachers.
Adults Surviving Child Abuse president Cathy Kezelman said the church still needed to be more transparent and forthright about its role in the systematic abuse of children over the years.
"It's an absolutely minimal response to express regret," she said on Monday. "It's very important that we also acknowledge the failure of religious organisations, including the Catholic Church, to respond appropriately to victims."
Last week, the federal government announced the terms of reference for the royal commission would not be available until January, instead of this month.
The inquiry is due to begin in 2013 and could run for years.