Mr P.J. Mara, who quit as Fianna Fáil's director of elections for the Nice campaign yesterday, had been found "totally innocent" by the Flood tribunal, the Taoiseach, Mr Ahern, has said.
The Taoiseach downplayed Mr Mara's loss from the upcoming campaign, saying that most of his work had "already been completed".
"The fact is that P.J. Mara, who is a very hard-working individual for Fianna Fáil, has been found innocent of the offences that were put before him.
"That is the fact. But he has been reprimanded in the lowest scale because his affidavit was not complete. And he has accepted that fully and accepted that he could not be director of elections," he said.
Rejecting Opposition calls to resign, Mr Ahern told the Newstalk 106 radio station: "I never felt that when John Bruton appointed Michael Lowry that that was a resigning matter either."
The Taoiseach's decision to allow Mr Mara time to quit his post, rather than be fired, led to a barrage of criticism throughout yesterday from the Opposition.
In a brief statement, Mr Mara, who also led Fianna Fáil's general election campaign, said the upcoming referendum "is fundamental to the future of both Ireland and Europe".
"I am determined to ensure that nothing relating to me could be used in an attempt to damage the chances of a successful outcome to the campaign," he declared.
Fianna Fáil said Mr Mara had told Mr Ahern, the Minister for Foreign Affairs, Mr Cowen, and a number of advisers late on Wednesday evening that he would resign.
"The decision was made to allow him to go in his own time. We knew that he would do it as early as possible," one Government source told The Irish Times.
The Minister for Foreign Affairs, Mr Cowen, who has replaced Mr Mara as director of elections, spoke to many Fianna Fáil TDs yesterday to order a wide Yes canvass this weekend.
"Look, we can't bury our hands in the sand. People have to go knocking on doors and take the criticism. We have to face it head on," said a senior Government source last night.
Describing the Mara resignation as "inevitable" and "necessary", the Labour Party's deputy leader, Mr Brendan Howlin, said the episode illustrated Mr Ahern's "lack of political backbone".
Mr Pat Rabbitte of Labour said the attempts by Mr Ahern and others to suggest "that Ray Burke was some sort of a one-off" are "disingenuous and very wide of the mark".
Fianna Fáil should now immediately reveal how many people listed as having obstructed the Flood tribunal are party members and whether they have made contributions to it.
The Green Party chairman, Mr John Gormley, said the resignation was "a very serious blow to the Yes campaign" and displayed Mr Ahern's "indecisiveness and moral cowardice".
Speaking in Cabra, the Taoiseach insisted he had not been bullied by the Opposition into setting up the Flood tribunal: "It was my idea. I was under no pressure whatever," he declared.
However, Mr Rabbitte said Mr Ahern is now trying to "rewrite political history" by claiming that he "single-handedly" set up the tribunal "that nailed Ray Burke".
"The truth is very different. The truth is that the tribunal had to be forced out of a reluctant Taoiseach and government by the opposition parties," Mr Rabbitte added.
