The Taoiseach was heavily criticised in the Dail yesterday over his remark on RTE television that the Spencer Dock development would be "a monstrosity" if it went ahead as planned.
The Fine Gael leader, Mr John Bruton, said the Taoiseach had "behaved entirely improperly" and should apologise to An Bord Pleanala.
"It is entirely wrong that issues before an oral hearing are now being politically prejudiced by the Taoiseach for reasons that are unknown," Mr Bruton said.
During a profile of Mr Ahern by RTE's Charlie Bird, broadcast during the Six One News on Wednesday, the Taoiseach could be heard saying to a constituency worker: "I mean the CitiBank site is high. Could you imagine if the other thing was there? It would be a monstrosity. We don't need skyscrapers."
The leader of the Labour Party, Mr Ruairi Quinn, said the Taoiseach's comments could contribute to litigation against the State by the developers if they failed to get planning permission.
He called on Mr Ahern to "consider clarifying the matter so as not to prejudice the outcome and give succour or comfort to any party which may feel aggrieved if the ultimate decision of An Bord Pleanala goes against their interests".
The Taoiseach said he did not believe he had "made any great pronouncements of Government policy".
"My views in support of a conference centre are on record and I have in many interviews given my views on the height of the building."
Mr Bruton said Mr Ahern had voiced his reservations about the project not "as a public representative, which could have done by means of a third-party objection", but "in a fashion where all the people involved are now prejudiced in the work they have done".
Mr Bruton continued: "What is the point of having a planning appeals board if the Taoiseach, by off-the-cuff comments of that nature, prejudices all the money spent by all the people concerned before that body?".
Mr Quinn said legal advice was "urgently needed and corrective measures should be taken by the Taoiseach so as not to add to the saga of litigation which already surrounds this project".
The Taoiseach replied: "If what Deputy Quinn suggested were helpful in some way, I could certainly do that".
A spokesman for the developers of Spencer Dock declined to comment on the controversy.