The Taoiseach has told the Dáil that the transition from paramilitarism to exclusively democratic means needed to be clearly advanced "towards a definitive and unambiguous end-point".
Outlining developments required to rebuild trust among the parties in the North, he said: "Transition also involves clear obligations for loyalism."
There was also a need to clearly demonstrate that the Belfast Agreement "remains the template, that the two governments intend to fully deliver on its provisions, and that we are not for turning on our commitment to its fundamental values and principles".
Mr Ahern, who was opening a debate on Northern Ireland, said he had always been willing to acknowledge the major contribution of the Sinn Féin leadership to the peace process.
"And I would like to do so again here this evening. Their key role in persuading the IRA to call a ceasefire, agree to independent arms inspections and undertake two acts of decommissioning have been essential to creating the conditions for a political process and for sustaining it.
"This summer's IRA apology was also an important and welcome development." Moreover, he said, Sinn Féin had itself undertaken a number of initiatives designed to build greater confidence, including Mr Alex Maskey's commendable outreach to unionism as Mayor of Belfast.
"Unfortunately, the confidence-building potential of these actions has, to a great extent, been dissipated by a number of confidence-eroding events, including the most recent arrests. There is no escaping the reality that these have caused damage and affected confidence.
"The fact of the matter is that, eight years after the first IRA ceasefire and 4½ years after the agreement, people in Northern Ireland have a legitimate expectation that the transition to exclusively democratic methods should be much more advanced than it is today."
Mr Ahern said that the loyalist community had suffered greatly over the years. A number of its political leaders, particularly within the PUP, had made important contributions to the peace process and had shown great political courage and leadership.
"The Government wants to have a relationship of mutual respect and partnership with loyalism. However, those godfathers of violence within loyalism, who seem only to be motivated by sectarian hatred and their self-enrichment, merely impoverish their own community, as well as inflicting suffering on the nationalist community." Mr Ahern said that the outcome of the Ulster Unionist Council meeting in September represented the emergence of a "deeply disappointing" policy to many nationalists.
It had created a perception that leading elements within unionism were seeking to turn back the clock on the agenda for change represented by the agreement. The fall-out from the arrests, and the related search of the Sinn Féin offices in Stormont, accelerated a political crisis which was already evolving and would, in any event, have come to a head in January.
"However, they also raised very serious issues of trust and confidence. For many unionists, who supported the agreement and wanted this accommodation to work, recent events were the final straw." On demilitarisation, he said that while progress had been made, he believed there was scope for doing a good deal more.