Media speculation about the reasons for Mr Justice Flood's resignation from the Flood tribunal was described as "simply incorrect" by the Taoiseach.
"Members of the House have received his letter of resignation and we should accept and respect this decision," said Mr Ahern.
The Taoiseach read to the House the text of a letter sent to him by Mr Justice Flood on Monday in which the judge had referred to public press statements to the effect that action/inaction by the Government relating to requests from the tribunal for additional judges or other matters had caused frustration and were the real reason for his resignation.
Mr Justice Flood had added: "I wish to state categorically that this is not so. My decision is in no way related to or consequent upon any action or inaction by the Government of any kind."
Mr Ahern also revealed that at the tribunal's request a meeting between the Attorney General, Mr Rory Brady, and Mr Justice Flood, Mr Justice Mahon and Ms Justice Faherty had taken place on May 26th.
This related to Mr Justice Mahon deciding costs as a new chairperson and Mr Justice Flood becoming an ordinary member.
The Labour leader, Mr Pat Rabbitte, said that if the Attorney General was "seized" of the matter on May 26th, surely he had a clear opinion by the time he went to Cabinet last week in terms of whether the taxpayer was likely to be exposed to horrific costs for people considered to have obstructed the tribunal.
"I am sure the Taoiseach agrees with me that if the taxpayer ends up paying €10.5 million in fees down the road for Ray Burke, there will be outrage in this country," he added.
Mr Ahern said costs were a matter for the tribunal.
Earlier, the Taoiseach, responding for a demand for clarity from the Fine Gael leader, Mr Enda Kenny, said that matters had changed over the weekend.
"There is no problem with the tribunal continuing its work. The matter of costs is the issue which requires legislation, which can be done in the autumn," he added.
He said he had made clear in the Dáil last week his preference that Mr Justice Flood would decide the costs issue.
"We took the view that if Mr Justice Flood proceeded to deal with other modules, and not address the costs issue, because of the reasons set out in his letter on June 16th, it would appear to be at risk that people appearing in these modules could rely on this fact as potential grounds for legal challenges," he said.
The Government had sought further clarification from Mr Justice Flood on this aspect of his proposal. However, this was overtaken by events.
He said that on June 26th a meeting had taken place between the Attorney General and Mr Justice Flood at the judge's request to clarify his position.
The judge had stated that he was personally disposed towards dealing with the issue of costs and, indeed, to carry on in the tribunal for a further period.
He had also stated his willingness to address the costs issue, notwithstanding the added strains burden it would impose. There was also a brief discussion about possible future legislative changes to enable the administrative burden of the tribunal placed on a chairperson.
Later, the Attorney General was informed by Mr Justice Flood that he wanted to reconsider his future role in the tribunal having had further discussions, said Mr Ahern. Last Friday, the Attorney General received a telephone call from Mr Justice Flood that he was resigning from the tribunal.
Mr Ahern said the decision was made "in the interests of the tribunal and its work to date and into the future," and he understood an appreciated it. Mr Kenny said it was important that there be absolute clarity about the issue. "Whatever else about their views on the tribunal, there is one thing very clear from the public perception," he added.
"That is the public do not want the taxpayer to have to take up the costs of those who were deemed to have clearly obstructed the findings of the tribunal, whether they be €10,000 or €10 million."
