The former minister for finance, Mr Charlie McCreevy, will remain Ireland's nominee for European Commissioner, the Taoiseach told the Dáil.
Mr Ahern said, with the deferral of the vote in the European Parliament on the new EU commission, "we have entered uncharted territory".
The Taoiseach added that the Government would support the commission president-designate, Mr Jose Manuel Barroso, in his efforts to find a resolution to the impasse.
The European Parliament was set to reject the entire 25-member commission over the appointment of Italian Mr Rocco Buttiglione to the Justice, Security and Equality portfolio because of his controversial views on homosexuality, single mothers and the role of women.
"With the deferral of the vote, we've entered chartered water. I regret it's not possible to complete the appointment of the new commission as planned," Mr Ahern said.
He said the present commission under President Romano Prodi would continue in office to allow the consultations take place. Mr Ahern stressed that "there is an issue only about one nomination".
Fine Gael leader Mr Enda Kenny, who raised the issue, called for a Dáil debate on the issue to allow everyone to state their views before Mr Ahern and other EU leaders meet as heads of government.
Labour leader Mr Pat Rabbitte asked would the Taoiseach "facilitate Mr McCreevy if he comes back".
Mr Ahern said that "obviously, the former minister, Mr McCreevy, will remain the Irish nominee for commissioner".
