The Minister for Foreign Affairs has said the two governments can begin implementing all elements of this week's Joint Declaration on the North, including demilitarisation and devolution of policing, before a political deal.
Speaking at a meeting of EU Foreign Ministers in Rhodes, Mr Cowen said the Good Friday agreement allowed the governments to take action in the absence of an institutional framework.
"What's set out there are intrinsic aspects of the agreement. The agreement is not simply about establishing institutions. It is a blueprint for the normalisation of relations within the island, between the communities on the island and between the two islands. That is an ongoing project.
"There are changes and reforms envisaged in the agreement which are not yet completed, and have to be proceeded with."
He said the Government had agreed to partial policing reform after the Weston Park talks on the understanding that further reforms were to come.
Mr Cowen said although demilitarisation depended on security assessments, which would have been enhanced by acts of completion on the part of the IRA, action was still possible.
"It is a far more benign security situation and one that is improving all the time. Therefore, one has to take account of that. Indeed, the British prime minister in his statement yesterday stated that there were issues in that policy area that he would move on."
Two British army watchtowers in south Armagh are to be taken down following Thursday's Joint Declaration and the most recent security assessment.
They are at Cloghogue, overlooking the main Dublin-Belfast road between Newry and the Border, and at Tievecrum. The move is opposed by the local Ulster Unionist representative, Mr Danny Kennedy.
Mr Cowen said the five-year review of the Good Friday agreement due in the autumn should go ahead. However, he said the review could not be used to dismantle elements of the accord.
"That's not about renegotiating the agreement, it's about reviewing the existing workings of the agreement, and how you can best implement what's in the agreement."
