The Taoiseach said that he had a short meeting to discuss "other matters" when he met the EU Commissioner in Brussels on Wednesday.
Mr Ahern was replying to Opposition demands that he tell the Dail if he had discussed with Mr Padraig Flynn the motion passed by the House that the Commissioner respond to the allegation that he received £50,000, which Mr Tom Gilmartin says was meant for Fianna Fail.
The matter was first raised on the Order of Business by the Fine Gael deputy leader, Mrs Nora Owen.
"Will the Taoiseach tell the House what opportunity he had yesterday in Brussels to discuss the motion with Commissioner Flynn? Did he get an opportunity to have a one-to-one meeting with Mr Flynn to discuss the matter?
"Will he clarify the discrepancy between Mr Flynn's assessment of what he said to the Taoiseach and the Taoiseach's assessment?"
The Labour leader, Mr Ruairi Quinn, said he had been told by the Taoiseach on Tuesday that he had no specific plans to meet Mr Flynn on Wednesday.
"When were the changes in the plans made and when was it decided that the Taoiseach would meet Commissioner Flynn?"
Mr Ahern replied: "I stated in the House during the extended Question Time on Tuesday that my understanding was that Commissioner Flynn would be returning from America on Wednesday and that if it was possible we would meet, but that we had no confirmation of a meeting, as his senior officials were with him.
"Very late on Tuesday night his office stated that he would be back in time and would meet me after the Commission meeting and before I met the President of the Commission, Mr Santer. This was communicated to me on Wednesday morning at the airport.
"We met for 50 minutes before I met President Santer and we discussed issues surrounding Agenda 2000. As I said last night on RTE and to the media, I had a short meeting of about three minutes on other matters."
When Mrs Owen pressed the Taoiseach to say if officials had been present during the three-minute meeting, the Ceann Comhairle, Mr Seamus Pattison, said that the matter could not be debated on the Order of Business.
Persisting with her questions, Mrs Owen asked if the Taoiseach had relayed to Mr Flynn the House's annoyance and anger that his letter to Mr Ahern did not reply to the motion passed by the Dail.
"Commissioner Flynn is fully aware of what was said in the House on Tuesday," the Taoiseach replied.
Mr Quinn said he was sure everybody in the House would like some clarity on the matter.
Mr Ahern replied: "In whatever matters the (Flood) tribunal request of him (Mr Flynn), he will fully facilitate its investigations."
Geraldine Kennedy writes:
Fine Gael has sought clarification from the Flood tribunal of the legal advice preventing the EU Commissioner, Mr Flynn, from making a full statement about the £50,000 donation which he allegedly received from Mr Tom Gilmartin in 1989.
The chairman of the parliamentary party, Mr Phil Hogan, sent a letter to the tribunal yesterday asking for a response as quickly as possible.
Pending clarification of this matter, Fine Gael has further postponed a decision on whether to table a motion of no confidence in, or censure of, Mr Flynn in private members' time in the Dail next week. The motion would have to be tabled this afternoon.