The Taoiseach said there was "no agreement or understanding between the Government" and either Ms Beverley Flynn and Mr Michael Collins.
Ms Flynn was expelled from the parliamentary party and the party, while Mr Collins resigned from the parliamentary party.
Mr Ahern was asked by the Fine Gael leader, Mr Enda Kenny, if an official in the Taoiseach's Department dealt with any independent members on a regular basis, as was the case in the past.
"One member of staff continues to deal with independent members, but not to the same level or extent as during the lifetime of the previous government because of the circumstances pertaining to it. I have not cut off the courtesies show to the people who supported the previous government."
When Mr Kenny pressed the issue, the Ceann Comhairle, Dr Rory O'Hanlon, said the questions referred to Ms Flynn and Mr Collins.
Mr Seymour Crawford (FG, Cavan-Monaghan) remarked: "They are now spare wheels rather than full wheels."
Mr Ahern said the previous administration, a minority government, had a formal arrangement under which the official in question spent quite an amount of time briefing certain deputies on what was due to arise in the Dáil.
"That system was not carried over into this administration. However, when those deputies raise important issues, which is a regular enough occurrence, we endeavour to assist them.
"This does not involve deliveries being made, and it is a normal courtesy. It is a service that I am always prepared to extend to other deputies as well."
When Mr Tom Hayes (FG, Tipperary South) remarked that all deputies would appreciate some of that service, Mr Ahern said he had never walked down the corridor without extending that facility. "I even extended it to a few members yesterday."
Green Party leader Mr Trevor Sargent said Ms Flynn and Mr Collins might no longer feel as close to the party as before, but they were still very much of the family.
