The Taoiseach reiterated that he first knew of the £50,000 given to Mr Padraig Flynn when it became public knowledge.
Mr Ahern said the cheque was made out by the property developer, Mr Tom Gilmartin, to cash, and not to the Fianna Fáil party.
"I first knew about the issues when Mr Gilmartin put it on the public record that he had given Padraig Flynn resources, and the matter has been subject to investigation since."
Answering Opposition leaders' questions, he said the cheque was subject to dispute.
"Whether it was in a bogus account in the Isle of Man, in Jersey or anywhere else, I do not know. That is a matter for the tribunal."
People had said that he should answer for Mr Flynn's finances. "I know no more about them than Deputy Rabbitte or Deputy Kenny would know about any of the issues which came up over the years in their parties.
"I do not particularly want to know about them, but the tribunals have full responsibility to find out about all of these issues. I am sure they are already in the process of uncovering them, so far as I can see and hear."
He said no offer had been made to repay the money.
Asked if the party had endeavoured to get the money back, Mr Ahern said the then Fianna Fáil general secretary, Mr Martin Mackin, had written to Mr Flynn in 1998 about the issue. He had subsequently put the contents of the letter on the record of the House, and sent it to the tribunal.
Asked if Mr Flynn had replied "substantively" to the letter from Mr Mackin, the Taoiseach replied that Mr Flynn had not "comprehensively" answered the issue, and had stated publicly that he would address it within the tribunal. "That is where it has been for the past five years plus."
He added that the party's position was that, at the end of the tribunals, the party would take whatever action deemed necessary.
He said the Minister for Justice, Mr McDowell, had said he had concerns about issues in the public domain for some years. "Everybody had concerns about them."
The Labour leader, Mr Pat Rabbitte, said for a serving Cabinet Minister to open a non-resident bogus account in Castlebar "is a disgraceful disservice to his office".
He added that having regard to the fact "that the serving Cabinet Minister gave a London address while still in the Cabinet and falsely signed a revenue form is a disgraceful betrayal of the confidence placed in him by the public". He added that in 1989 £50,000 would have bought two houses in his Dublin South West constituency.
Mr Ahern said there should be no doubt about his position. "Tax evasion is wrong. Encouraging anybody to engage in tax evasion is wrong."
He said Ms Cooper Flynn was entitled to make a statement to the House. "She is neither above nor below the law. She is entitled to due process."
He added that neither himself nor anybody else should rush to judgment. Ms Cooper Flynn had appealed a court case, and it was on that basis that she had been readmitted to the Fianna Fáil parliamentary party. "We await that appeal."
He would not be suing the newspaper which made an allegation against him about the tribunal. "I have never sued a newspaper in 27 years in this House."
The Fine Gael leader, Mr Enda Kenny, said everybody in the House, and throughout the State, was aware of the damage being done to public confidence and the democratic process from the torrent of revelations emanating from the various tribunals.
"People are disgusted by the litany of wrongdoing exposed by numerous of the Taoiseach's former and current colleagues, and the way they would appear to be privately accommodated and protected by Fianna Fáil."
Mr Caoimhghín Ó Caoláin (SF, Cavan-Monaghan) said many of those giving large donations to elected FF representatives had stated they were for the party and had made it clear to the recipients, including Mr Flynn.
