The Taoiseach, Mr Ahern, said the then general secretary of Fianna Fáil wrote to former minister Mr Pádraig Flynn in 1998 to try to retrieve a cheque for £50,000.
Mr Ahern told the Dáil this evening that Mr Martin Mackin wrote to Mr Flynn to ask him to confirm he had received the cheque from builder Mr Tom Gilmartin in 1989. Mr Gilmartin claims he gave Mr Flynn the cheque as a political donation to the party, but it never found its way into Fianna Fáil's coffers.
The Taoiseach said Mr Flynn did not "comprehensively" answer the questions posed in the letter and said he would being addressing the matter at the Mahon Tribunal.
In response to a question from the Labour Party leader, Mr Pat Rabbitte, the Taoiseach said the cheque was made out to cash, rather than to the Fianna Fáil party, as previously claimed.
The cheque was never recovered, and Mr Ahern said it was now a matter for the tribunal. "The Fianna Fáil position is that on the conclusion of the tribunal ... we will consider legal advice and take whatever action that we deem necessary.
"I have at all times assisted the tribunal in every way I could," he said. "I am not going to run a parallel inquiry."
"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," he said.
"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."