Support for the Belfast Agreement remained "fundamentally sound," the Taoiseach told the House.
Mr Ahern said difficulties had been highlighted and there might be a sense among sections of the unionist and loyalist communities that they were losing out.
"However, reports of discussions with them indicate that they accept an enormous amount is being achieved, and, while there is some violence, it is sporadic and a level of reconstruction, regeneration and improvement with a positive approach is also present." Mr Ahern, who was replying to the Labour leader, Mr Ruairí Quinn, said it was the job of both governments to give confidence and support in practical ways.
"I accept that there are some elements within the unionist-loyalist community who have the view that things are not as good for them. I equally accept that the people of the Short Strand, who have seen their community dwindle considerably because of the difficulties over the years, also feel that they are under huge threat. Such feelings are not mutually exclusive.
"The key issue is that we must maintain momentum in the process and do all we can by working closely with the pro-agreement parties and other parties, where possible, to ensure that the implementation is fair and to the letter of the agreement."