The Taoiseach has told the Dáil he accepts the conclusions of the Moriarty tribunal that the practice of pre-signing cheques drawn on the Fianna Fáil party leader's account was "undesirable".
However, during statements in the House on the recent tribunal report, Mr Ahern said it was a "not uncommon" practice in past decades and he outlined major changes in ethics legislation since he engaged in the practice.
Taoiseach Bertie Ahern
Mr Ahern said there were now a "large number of restrictions" and guidelines as to how the money in the party leader's account could be used.
"We have learnt much from the work of this tribunal and from its predecessor the McCracken tribunal," he said.
"What came home very forcefully to me as I read this report is the sheer scale of the amounts of money - over €11 million (or some €45m in today's values) - found by the tribunal to have been either privately donated to Mr Haughey or misapplied by him during the period under inquiry from 1979 to 1996," Mr Ahern said.
"What struck me even more forcefully were the devices employed to conceal the fact of and the nature of those transactions.
"We are indebted to Judge Moriarty and the Tribunal team for their outstanding work in painstakingly stripping away the layers of secrecy and obscurity surrounding Mr Haughey's financial affairs and exposing them to public scrutiny. We look forward to receiving the second part of their report soon.
Mr Ahern said the revelations had come as "a grave disappointment" to those who knew and worked with Mr Haughey over the years.
"Even now, I and others who worked with him in government find it difficult to comprehend the complexity of the man and the other life he led."
Quoting Mr Justice Moriarty's statement that the events upon which he reported had "devalued the quality of modern democracy", Mr Ahern said this was a "harsh and damning indictment". "It is also a great tragedy."
He said he stood over his own criticisms of Mr Haughey at the 1997 Fianna Fáil ardfheis and in subsequent interviews.
"I also stand over my comments made at Mr Haughey's funeral and on other occasions that he did a lot of good work for this country."
Fine Gael leader Enda Kenny
The Opposition parties failed to secure extra time to debate the contents of the Moriarty tribunal report, which was published just before Christmas and which was highly critical of former taoiseach Charles Haughey
Fine Gael leader Enda Kenny said the report was a "devastating critique of a powerful elite" and that it exposed "devastating abuses of public trust".
Mr Kenny said the report is "a bleak but essential analysis of the relationship between politics and business and what posed as -and passed for - national leadership in this country, in worryingly recent times".
"It is a devastating critique of a powerful elite, exposing a gross abuse of privilege, a rank abuse of public office, and most importantly of all, a devastating abuse of public trust," Mr Kenny said.
"Justice Moriarty returned a devastating verdict on the late taoiseach Haughey. However, to see Mr Haughey's behaviour as an aberration within FF, would be an affront to the tribunal, and indeed, to every democrat in this country.
"Because far from being an aberration, Mr Haughey's behaviour and attitude typified the culture of FF at a significant period. Where Raphael P Burke, accepted corrupt payments related to radio licences, where there was serious corruption of the planning process, and where funds, donated to FF for the practice of democratic politics, were misappropriated."
Mr Kenny later added: "Until the current senior members of FF are willing to acknowledge the wrong and the damage done to public confidence in politics, it will not be possible for them to make a clean break from the culture of corruption that enveloped their party for such a long period."
Labour Party leader Pat Rabbitte expressed concern that there would be only a "truncated debate" on the "profound issues" raised by the Moriarty report into payments to politicians, including the former taoiseach and Fianna Fáil leader, the late Mr Haughey.
Mr Rabbitte recorded his thanks to the tribunal chairman Mr Justice Michael Moriarty and his team.
"Despite the attendant reservations that must accompany the publication of a document that was in fact commissioned almost 10 years ago, I believe this report is important," he told the Dáil.
"It, together with the McCracken report which immediately preceded it, goes some way to rescue our democracy from growing uneasiness that a small group of powerful and wealthy individuals had come to regard themselves as the beneficial owners of the State, while nobody in authority was prepared to call a halt," Mr Rabbitte said.
"The findings of this, the first report of the Moriarty Tribunal, represent a damning indictment. And it's an indictment not just of the record of Charles Haughey but also of the entire political culture in Fianna Fáil during the period when he dominated that party.
"It is the reason that a new conventional wisdom has grown up that Fianna Fail cannot be let out without an escort. Even those likely to support that party don't trust them to govern alone," Mr Rabbitte said.
Mr Rabbitte said the report was "a sorry tale of misuse of taxpayers' money, the placing of public servants under pressure to do the will of the then Taoiseach, and a group of craven colleagues who were unwilling to challenge his writ".
Arthur Morgan of Sinn Féin and independent TD Finian McGrath have also made statements to the House.
There will be a time limit on statements to the House on the matter and they are to conclude by 1.30pm.