The Bishop of Cork and Ross moved to distance himself from comments made by the priest, who asked that former Lord Mayor of Cork John Murray be found not guilty.
Bishop Dr John Buckley described the comments as "offensive and inappropriate" and that he expects the priest's order to address the issue.
The priest, who is not assigned to the diocese, apparently called for prayers for Murray (83) who was facing a trial in the Circuit Criminal Court on six charges of sexually assaulting a young teen.
Murray, who served as Lord Mayor of Cork in 1993-94, was convicted on five of the six charges last Friday.
The veteran Labour Party official had vehemently denied the charges but was convicted by unanimous jury vote on one charge and by majority jury vote on the remaining four charges.
The retired taxi driver was remanded in custody for sentencing before Judge Sean O Donnabhain on December 2.
Last night, the Diocese of Cork & Ross strongly disassociated itself from the priest's reported comments at a Requiem Mass outside Cork city last week.
The comments were made before the jury had begun to consider their verdict.
"Dr John Buckley says he does not stand over comments made at a funeral in Cork last week," a spokesperson said.
The comments involved, which were made during the Prayers of Intercession at the funeral, were described by the diocesan spokesman as "offensive and entirely inappropriate".
"The Dioscese was unaware the comments were going to be made and the Bishop says he doesn't stand over them and sincerely regrets the obvious hurt they have caused."
Dr Buckley has since moved to deal with the issue. Diocese officials "have been in touch with the priest's order and expect them to address the issue", said a statement.
"The diocese fully respects the independence of the DPP and Courts Service and it is inappropriate that a funeral Mass should be used in such a manner."
The victim of the sex assaults, who was a young teen at the time of the first offence in 1996, sobbed as the verdicts were returned.
She repeatedly broke down during her evidence at the trial where she outlined the details of the sexual assaults she was subjected to.
She said the former Lord Mayor whispered that she was "a very beautiful girl" and that he "would love to f*** her".