The Taoiseach insisted that Mr Ned O'Keeffe resigned voluntarily as Minister of State for Agriculture. Mr Ahern was replying, on the Order of Business, to repeated Opposition requests that he make a statement on the resignation.
Mr Ahern said: "It is the Taoiseach's job to hire and fire. Deputy O'Keeffe resigned as a minister of state and I appointed somebody in his place. End of story."
Earlier, Mr Ahern had been accused of being "a coward" by the Labour leader, Mr Ruairi Quinn.
Pressed by the Ceann Comhairle, Mr Seamus Pattison, to withdraw the term "coward", Mr Quinn said he would, adding that he would not allow Fianna Fail backbenchers to bully him into silence.
"Deputy Ned O'Keeffe was bullied into resigning. The Taoiseach misled the Dail and has consistently refused to explain what happened." The Fine Gael leader, Mr Michael Noonan, said the Taoiseach and everybody else in the House were aware that food safety and animal health were paramount at present.
"Yet, we have witnessed the unexplained resignation of the Minister of State who was responsible for food safety. Several precedents exist for Taoisigh and Cabinet ministers to come into the House to make statements and answer questions from the Opposition. Why is the Taoiseach so afraid to follow precedent in this regard? Has he something to hide?"
Mr Ahern said the Minister of State for Health, Dr Tom Moffatt, was in charge of food safety and there was no dispute about him.