There was every reason to believe that decommissioning issues would be resolved through the intensive contacts and dialogue now under way, according to the Taoiseach.
In a message to mark the passage of today's missed deadline for the establishment of the Northern executive, Mr Ahern said the decks had now been cleared and the disagreements over detail resolved. "This is not the end but the beginning, and as the institutions develop they will inevitably break new ground to the real benefit of both parts of the island," he added.
Earlier in the Dail, Mr Ahern had challenged the Sinn Fein TD, Mr Caoimhghin O Caolain, "not to talk up a crisis" in the peace process.
He also told Opposition leaders he was "not a party" to the Northern Secretary's decision, in consultation with the British Prime Minister to set a new deadline of the week before Easter for setting up the Northern executive.
He later explained to Mr Ruairi Quinn that, while not wanting to make too much of this, the first he had heard of the deferred deadline was Monday evening.
"A Sinn Fein staff member, who was in a corridor with Mr Adams, informed me about this," he said.
Stressing that the Taoiseach did not wish to make an issue of it, Government sources said Mr Ahern had expected Dr Mo Mowlam to wait until after today to set a new target date.
During the debate on the British-Irish Agreement Bill, 1999, which ratifies four new British-Irish treaties, Mr Ahern said the six North-South implementation bodies would have chief executives.
The bodies, when up and running, would have a total staff of 880 and cost £56 million annually, with £42 million of this to be borne by the Republic and £14 million by the North.
Four of the six new implementation bodies - food safety, trade and business development, language and aquaculture and marine - will have boards. The Food Safety Promotion Board will be of an advisory nature. The Special EU Programmes Body and the Waterways Ireland Body will be executive agencies headed by chief executives.
The committee and remaining stages of the Bill will be cleared in the Dail tonight.