Simon Harris made the comments after Waterford Junior Minister John Halligan said he was blocked from being a sponsor to his godson at a recent confirmation.
Bishop Alphonsus Cullinan says he instructed priests to make sure sponsors were "a good example of what it means to be a disciple of Christ".
Mr Halligan is an atheist and has been campaigning for a Yes vote in the abortion referendum.
Health Minister Simon Harris says some events shouldn't be affected by the debate.
He says it's disappointing what he is hearing from around the country in recent days, some ceremonies that are meant to be a very significant occasion in a young child's life, be it a communion or a confirmation have been used to bring about a discussion on the abortion debate.
He said he did not think that was appropriate on either side.
