Partnership government "is not there at the whim or favour of the Unionist party leadership", the Minister for Foreign Affairs told the Ardfheis.
In sharp criticism of the UUP leadership, Mr Cowen said that it was "not acceptable for a unionist party to put members on the Police Board as the Patten Commission recommended, and then fail to state that they are committed to the implementation of its recommendations".
The institutions "must be worked to their full potential in the interests of all the people. The reformed police service must now go ahead so that the Patten Report is implemented." The "new beginning on policing must be real and substantive. It is critical to the normalisation process and the creation of a truly pluralist and egalitarian society."
He said that republicans could not opt out of their responsibilities either to participate in the process of change that police reforms now envisaged. "The vision of the Patten Commission is available if everyone who has a stake in the community is prep ared to take on the responsibility of working hard to achieve it."
The context of policing in Northern Ireland "can no longer be a predominantly counter-terrorist force. The preparedness to change all of these things in addition to the substantive work that has already been done will be a decisive factor in ensuring the early success of this all-important project."
He congratulated the SDLP "for having the courage to recognise that the time has come to participate rather than to protest". Mr Cowen also paid tribute to the party's leader, Mr John Hume, and deputy leader, Mr Seamus Mallon, who are stepping down. "John and Seamus have been giants of the peace process. Each has made his own distinctive and enormous contribution."
Putting arms beyond use was an indispensable part of this agreement, he said. "The shackles of suspicion that retaining illegal arms represents can be cast off." The full potential for peace was "best guaranteed by those who had adhered to a militant tradition to finally confirm that exclusively peaceful and democratic methods now provide the only means to effect peace, reconciliation and self-determination on this island." By transforming the political atmosphere "you will oblige all to proceed without further hindrance to full implementation of the Good Friday agreement".
No part of the community, "not least in loyalist areas, can have their concerns and grievances properly addressed by a reversal to paramilitary violence".
The Government was "calling on all those with influence in those paramilitary organisations to see sense and pursue exclusively peaceful methods in dealing with the problems of their communities".