In a written apology on the eve of Yom Kippur, he said the issue has been handled inappropriately with a culture of covering up abuse.
Rabbi Gutnick asked victims of abuse for forgiveness and urged them to come forward to ensure police can prosecute the perpetrators.
"We need to empower ourselves and victims to help to bring this scourge to an end," he said.
Talking to reporters, the rabbi addressed what he called a "cultural cover-up" with those inside the church refusing to contact the proper authorities in the belief sexual assault was a church issue, not a criminal one.
"I'm not talking about any specific incident or case. I'm talking about there was this idea of keeping the problem in house," he said.
"For something that was part of much of our thought processes and that again was completely wrong and we have to now be very open about what takes place."
He also acknowledged how a case he handled in 1987 has remained with him over the decades since.
"I received an anonymous phone call from a very young person telling me that they had been sexually abused," he said.
"At the time I reported it to the people involved but I didn't take it very seriously."
Rabbi Gutnick said he now regrets not taking action at the the time to catch and punish the perpetrator.
"If I would have done more, if I would have followed it up, if the perpetrator would have then been identified and caught, then there are many victims after that that would have been saved," he said.
In addition to the apology, the letter also addressed the behaviour of those inside the church, calling upon the majority of rabbi's to adopt a culture of forgiveness and reconciliation.
Tzedek, a group advocating for Jewish victims of child sexual abuse, has welcomed the letter, describing it as a ground breaking milestone for the Jewish community.
The founder and chief of Tzedek, Manny Weks, says an apology is an important step in the healing process for victims.
"I don't necessarily think that it is all of a sudden going to change overnight," he said.
"But it certainly does send out a very strong message that the peak body of the rabbinate and the orthodox community in Australia has taken an unequivocal position on this matter.
"It leaves no ambiguity on how they need to respond to this issue."