Mr Justice Flood has held talks with the Attorney General over his future role in the planning inquiry after the Taoiseach, Mr Ahern, urged him to determine which witnesses should have their costs paid by the taxpayer.
The judge met the Attorney General Mr Rory Brady yesterday after seeking such a meeting.
He has yet to formally respond to the Taoiseach's publicly stated view that he should hear the issue of costs to prevent any future legal challenges.
The meeting followed a recent request from Mr Justice Flood, who will be 75 next month, to stand down as tribunal chairman but remain on as an ordinary member of the inquiry.
Despite uncertainty over the scope of the tribunal's future investigations, the Government moved yesterday to dismiss speculation that it wanted to have the most politically sensitive evidence heard in private.
The Taoiseach and Minister for Justice, Mr McDowell, have suggested in recent days that parts of the inquiry could be heard in private by new commissions of investigation to be set up under legislation to be published next week.
However, the Taoiseach insisted yesterday that he believed there was no question that the highly politically-charged evidence of Mr Frank Dunlop and the London-Irish developer Mr Tom Gilmartin should be heard in private.
Mr Gilmartin has said that he met on a number of occasions with Mr Ahern.
A Government spokeswoman said last night: "It is neither the Government's intention nor the Government's desire that issues concerning Tom Gilmartin, Frank Dunlop and Padraig Flynn should be held in private."
Mr Justice Flood is believed to have been surprised at the Taoiseach's robust public statement that he should determine the costs issue.
In his recent letter to the Government seeking to resign as chairman, Mr Justice Flood specifically noted that he wished to avoid the strain of such work.
He suggested that Judge Alan Mahon, currently an ordinary member of the tribunal, become chairman and handle costs.
Government sources yesterday repeated their concern that if anyone other than Mr Justice Flood decided not to pay the costs of witnesses deemed not to have co-operated with the tribunal, such a decision could be open to a legal challenge. The judge who heard the evidence should decide the issue of costs, they believe.
There is particular sensitivity concerning the costs of the 15 witnesses about whom the judge made adverse findings.
The Government has yet to respond to a letter on Wednesday from the Flood tribunal - as distinct from Mr Justice Flood personally - in which it gave a prognosis for the likely duration of its inquiries.
Further correspondence from Mr Justice Flood on his personal situation is awaited.
With Mr Ahern stating this week that up to 15 years work might be required at a cost of up to €60 million, the tribunal is believed to have said that a considerable amount of work remained to be done.
Letters disclosed last night on RTÉ's Prime Time programme revealed that Mr Justice Flood told the Government three years ago that the tribunal was "in reality 10 tribunals in one".
The programme said Mr Justice Flood was then engaged in intensive dialogue with the Government over the provision of resources for the tribunal and its staff.
Mr McDowell said on the programme that he believed much of the work currently carried out by tribunal could be pursued by an alternative system of investigations.
"A lot of deep reflection must now take place as to whether this is an appropriate way to spend taxpayers' money," he said.
The commission of investigation system, to be considered by the Cabinet next week, would see detailed investigative work carried out in private.
In this scenario, the requirement to have expensive senior counsel carry out basic work would be diminished.