The issue of the release of the killers of Det Garda Jerry McCabe would have to be considered in the context of a final settlement in the North, the Taoiseach has said.
Mr Ahern said he expected that, at the end of the negotiations, the issue would be completed and dealt with.
"One of the original five was released and, obviously, others will be in prison for up to another five years. I know it is difficult for the families, but if we are to get an end to paramilitarism and violence and to work towards a constructive beginning, we must deal with this issue.
"Quite frankly, we must deal with this issue as part of the end game. It is not something to give away or trade off, but in the end this is where we would come to ultimately. I have made this clear to the Garda representative bodies."
Mr Ahern was replying to the Fine Gael leader, Mr Enda Kenny, who said that in his recent travels around the State, "the public expressed its concern about this issue, having voted for the Good Friday agreement in large numbers, on the strict understanding the release of these persons was not part of that agreement."
Asked by the Labour leader, Mr Pat Rabbitte, if recent remarks by the Minister for Justice, Mr McDowell, indicated a change in the Government's assessment of the republican movement, Mr Ahern said the Government had been assessing the movement. "I may be wrong, but I think even since last October, people are facing up to moving towards the end position. That will come to fruition only when matters are completed.
"The issues in the Joint Declaration, such as equality, policing and so on are very difficult."
It was not easy for the republican movement when it was not engaged directly with the DUP in talks, he said. "It is difficult for the DUP because of the history of the situation, but I increasingly detect from both sides a willingness to try.
"It will not happen overnight or over the next few weeks, but there is a willingness to do this. That is the belief of Government."
Mr Caoimhghín Ó Caoláin (SF, Cavan-Monaghan) said that the Assembly had collapsed on a number of occasions, due to unilateral action on the part of the British government, with which the Republic's government was supposed to be an equal partner in overseeing the implementation of the Belfast Agreement.
Mr Ahern said everyone wanted to see an end to the stopping and starting of the institutions. If he had managed to convince the British Prime Minister, Mr Blair, to get things moving just after Christmas, "it would have to come back down again through the actions of people associated with the deputy and his party." Mr Ó Caoláin replied: "The Taoiseach should withdraw that remark."