The Taoiseach, Mr Ahern, has written to An Bord Pleanala asking it to ignore his recent remark describing the proposed Spencer Dock development in Dublin as "a monstrosity".
The board concluded its oral hearing on the proposed scheme on Tuesday and is due to make a decision by mid-July.
In an exchange of correspondence released yesterday by the appeals board, the Taoiseach wrote to its chairman, Mr Paddy O'Duffy, referring to "comments attributed to me in relation to the National Conference Centre plan" in newspaper reports.
"I wish to point out that any such comments were made informally and solely as a Dail representative for the constituency in which the proposal is planned. They were not made as Taoiseach voicing Government policy, but rather as a personal comment."
In his letter, dated March 3rd, Mr Ahern said it was not his intention to influence any deliberations of An Bord Pleanala on the Spencer Dock development.
The letter concluded by requesting Mr O'Duffy to ensure that, in the board's deliberations on the appeal, "my reported comments do not in any way affect its independent judgment and are not taken into account".
In his reply, the board's chairman said its practice was to consider only submissions made in writing or at an oral hearing. "In the interests of natural justice, media reports on an appeal during the currency of an appeal are not considered.
"Accordingly, in considering appeals relating to the Spencer Dock development, the informal comments attributed to you in the media in relation to these appeals will not be taken into account and will not in any way affect the board's independent judgment."
Mr O'Duffy concluded by pointing out that the terms of his response to the Taoiseach had been endorsed by the board.
"I am also bringing the terms of your letter and the reply to the attention of the inspectors conducting the oral hearing on the Spencer Dock development."
In a brief statement accompanying copies of the correspondence, An Bord Pleanala said it was releasing the two letters because a reference to the Taoiseach's reported comments had been made at the closing session of the oral hearing. Mr Michael Smith, national chairman of An Taisce, said the Taoiseach had described the Spencer Dock scheme as "a monstrosity" and interpreted this to mean the National Conference Centre no longer had Government support.
The Taoiseach's remark, characterised by a spokesman for him as "unguarded", was made by Mr Ahern to his driver in the presence of an RTE in-car television camera and microphone. It was broadcast during the first week of the Spencer Dock oral hearing.