The Taoiseach, Mr Ahern, said Mr Bobby Molloy's decision to resign was a good decision and a brave decision.
He said his statement on Tuesday night that he did not consider the issue a resigning matter was designed to give Mr Molloy some time to reflect.
He said Mr Molloy contacting a member of the judiciary was "totally wrong procedure" and was a serious matter. There was no issue for the Minister for Justice, Mr O'Donoghue, in relation to the matter. Mr O'Donoghue's Department had received representations on the case and had responded appropriately.
Mr Ahern said that unlike other parties leaders it was not his practice to seek "a head on a plate".
"I don't like blood nor heads," he said. "I like to work hard and I think people who like to do that [look for resignations\], I hope they've done nothing wrong in their life and I hope they've never wrongly helped a constituent in their life."
Mr Ahern, speaking at the opening of a business centre in the Docklands Innovation Park, on East Wall Road, Dublin, said Mr Molloy had been endeavouring to help a constituent and to make representations about a letter.
"I think that in itself was not a resigning issue but to contact a member of the judiciary certainly is totally wrong procedure and I think everyone understands that. He was wrong in doing that and has accepted that."
Mr Ahern said Mr Molloy had wanted time overnight to reflect on that and he got the time to do that.
The Taoiseach said he appreciated Mr Molloy's contribution to the Government. "He worked for five years. He's done nothing wrong in his office. He has been an exemplary Minister, extremely hard working for 37 years and, I think people should understand this, he has worked as a minister and as a constituent politician, being re-elected all the time, giving excellent service. I think this is a personal tragedy for him and for Phyllis [Mrs Molloy\] and the family."
Mr Ahern told reporters Mr Molloy was a top class politician who was in Dáil Éireann "before most of you were born and I think we should not forget that today".
Asked if he had shown a lack of political judgment on Tuesday when he'd said Mr Molloy's actions were not a resigning matter, Mr Ahern said he had managed to make one phone call about the matter before making that statement and had not had all the details.
However, he said, he was "well aware of what was going on at that time, that Bobby Molloy was going to meet his wife and he wanted some time to reflect on it".
"If I had said anything else on it, you would have known what would be the headline and I would have been \ one of those leaders who have been out today, of the other parties, who make it a practice in Irish politics of looking for heads. It's not my part. I don't like blood nor heads."
Mr Ahern said his first sympathy and that of Mr Molloy was with the victim in the rape case. "People can be running around like headless chickens but the fact is that the victim in this is the really sad case. The second victim is Bobby Molloy."
Asked about the statement on the matter from the Department of Justice, Mr Ahern said Mr Molloy sent on a letter from the sister of the accused man to the Minister for Justice, Mr O'Donoghue. The Minister sent the normal reply "that you always get if you write on anything of a judicial matter".
Mr Ahern said he had not known until yesterday morning that Mr Molloy had received a number of letters from the accused's sister. He said he did not believe there was a problem with Mr Molloy sending these representations on to Mr O'Donoghue.
