The Taoiseach has accused the Ulster Unionist peer Lord Laird of being "disingenuous" and of hiding behind parliamentary privilege in claims he made about the financier Phil Flynn.
However, Lord Laird defended his comments - made this week in the House of Lords - and said he had a lot more information about Mr Flynn which he would make public soon.
He also claimed he had been deluged with messages of support, some from members of the Oireachtas, since he made his speech. "I feel like the boy who shouted that the emperor had no clothes," he said.
Mr Ahern and Lord Laird made their comments while addressing separate sessions of a conference at the Institute for British-Irish Studies at UCD yesterday.
In his House of Lords speech on Tuesday, the peer claimed that the Taoiseach "betrayed his own country" by allowing Mr Flynn to remain a close adviser while knowing he was associating with senior IRA figures.
He also claimed that the 2001 appointment of Mr Flynn as Irish chairman of the Bank of Scotland represented "the most serious breach of financial security by terrorists that has ever occurred within the United Kingdom".
Mr Flynn called the allegations "lies", and challenged him to repeat them outside parliament without the protection of parliamentary privilege.
Speaking to journalists at UCD, Mr Ahern also rejected Lord Laird's claims.
"I don't want to give too much prominence to someone with whom I disagree on everything he says. The comments that have been made are entirely untrue.
"They are entirely disingenuous. Phil Flynn has worked hard over many years, both in the trades union movement and in many other areas.
"The activities that he has now been accused of are under criminal investigation. Everybody should await the outcome, and not use parliamentary privilege to make such allegations."
However, Lord Laird, also speaking to reporters, said he would be returning to the subject of Mr Flynn in future comments with "a lot more information".
Some of this had been provided by people who had called him since his speech to congratulate him for "saying what needed to be said". He added: "I can't believe the reaction I've had to this from people in the South, including politicians."
He declined to comment on whether he would speak inside parliament or outside, but said he would not be dictated to by Mr Flynn.
A former chairman of the Ulster-Scots Agency, Lord Laird told the conference that the cross-Border bodies under the Belfast Agreement had been a failure.
His own agency had made a genuine attempt to wean loyalists away from paramilitarism and drug-dealing and into cultural pursuits, but had been thwarted by cuts in funding and a conspicuous lack of support from official bodies.
The "dysfunctional" nature of some cross-Border bodies had been a factor in the Ulster Unionists' electoral humiliation.