The Taoiseach said that Mr Liam Lawlor's vice-chairmanship of an Oireachtas committee must be considered.
Mr Ahern insisted it was a matter for the Joint Committee on Finance and the Public service to decide. "I have no difficulty discussing these matters, as I always do, with my committee. Fianna Fail will always make decisions when other people will not do so."
During heated exchanges with the Opposition, Mr Ahern rejected a Labour motion calling on the Dublin West deputy to comply with the orders of the Flood tribunal or resign his Dail seat.
He said his advice from the Attorney General, and other sources, was similar to the view given by the Ceann Comhairle, Mr Seamus Pattison, that the Dail could not encroach on the functions of the courts or a judicial tribunal.
"If the Dail was allowed to proceed with this motion, or a motion of like substance, it would, in your view, sir, be in breach of standing orders and the established precedents of this House since its foundation."
Mr Ahern said the tribunal was established by the unanimous will of the members of the House, "and every citizen, and even more so every member of the Oireachtas, owes a legal, moral and democratic duty to co-operate with the tribunal, not to obstruct it and to comply with its lawful order."
"We would expect any citizen, and any member of the Oireachtas who disputed the validity or legality of that tribunal order to make his or her case to the tribunal, and, if necessary, to the courts.
"As I was advised, I should not go any further than that, because it would be deemed to be interference, and I do not want to do that."
The Labour leader, Mr Ruairi Quinn, asked what could be of any more general public importance "than the travesty of a member of the House, which includes everyone else, citing as his reason for not complying with the directions of the courts, and the chairman of a tribunal, that because he was a member of the House and had facilitated the terms of reference of the tribunal, he had some right, by virtue of his membership of the House, not to co-operate with the directions of the chairman".
Earlier, the Fine Gael leader, Mr John Bruton, said Mr Lawlor was a Fianna Fail representative, appointed by that party, to the joint committee, which was responsible for ethics legislation.
As vice-chairman, he was paid an extra £5,000 annually.
"Fine Gael and I do not think he is a suitable person to be vice-chairman of this committee, notwithstanding the fact that he was nominated by Fianna Fail."
Mr Ahern said Mr Bruton was correct that Mr Lawlor was appointed in the first instance as a Fianna Fail member. "Now, of course, he acts as an independent member. I understand he did not resign and no effort was made to remove him. Obviously, that has changed and the position must be considered."