ABC News reports Archbishop Coleridge made his comments after a former teacher, Br John William Chute, 76, - who is also known as Brother Kostka - was jailed for two years this week following a guilty plea to molesting six students at the school in the 1980's.
The Marist Brothers have apologised to the victims.
Archbishop Mark Coleridge says, while there can be no guarantees, the Church is working hard to prevent any further abuse.
"I think we're doing our best, but sadly in this sort of area I can't sit here and say to you we've weeded out absolutely everyone and it's never going to happen again," he said.
"I wish I could say that and we'll do absolutely everything we can to make sure it happens, but I can't say it.
"But we are certainly doing our best."
Three civil claims have already been lodged in the ACT Supreme Court against the Trustees of the Marist Brothers and about 20 more are expected to be lodged by the end of this week.
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