The Bishop of Galloway used a pastoral letter to express his concerns at the crimes of Father Paul Moore.
Fr Moore, 82, was last week jailed for nine years for sexually abusing three children and a student priest over a 20-year period.
Bishop William Nolan said the trial had been “embarrassing” for Catholics and called into question “the trust they have in their priests”.
Five years ago a BBC investigation revealed Fr Moore had confessed the abuse to one of Bishop Nolan’s predecessors, Bishop Maurice Taylor, who sent the priest to a treatment centre in Toronto and then to Fort Augustus Abbey in the Highlands.
The diocese later reported the abuse to the police.
Bishop Nolan said: “These events may have happened decades ago, but the victims who suffered then are still suffering now since such abuse has long-term consequences.
“It is difficult to know how to help these victims and indeed all who have survived abuse, but we must make it our priority to do so.”
He added: “The diocese has also suffered from this affair. Since the allegations were made over 20 years ago, this affair has poisoned relationships among the clergy. There is still much healing required.”
Bishop Nolan said it could be argued the “greatest obstacle to preaching the Gospel” in Scotland was the Catholic Church itself.
“First and foremost I offer my sympathy to each individual victim of Paul Moore,” he said. “I also offer my sympathy to all the clergy of the diocese.
“You give your life for your people, working hard as you persevere in the daily grind of parish work, helping each other share the workload. But clergy morale is bound to be affected as yet another abuse conviction blackens the good name of all.”
Bishop Nolan said he had started the canonical process that would likely lead to Fr Moore being dismissed from the clergy.
Andi Lavery, one of Moore’s victims who has waived his right to anonymity, said the bishop’s letter was “utterly pathetic”.
He said: “He asks people to pray for Moore. Do we pray for paedophiles now?
“Reading that letter, it’s as if the bishop is the biggest victim.”
Last year the Bishops’ Conference used the Scottish Child Abuse Inquiry to re-iterate an earlier apology to survivors of sexual abuse.
Canon Thomas Boyle said the Church had “missed red lights and warning signs”, but had also been “deceived” by the abusers.