Mr Ahern said his government wanted to develop relations with loyalism
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A meeting between the Loyalist Commission and the Irish Prime Minister, Bertie Ahern, has been described as a "useful building exercise".
The taoiseach met members of the commission, which was set up to provide political analysis for the paramilitary groups and includes members of the main loyalist paramilitary groups, unionist politicians and the clergy, at an undisclosed location in Dublin.
The Church of Ireland Primate, Archbishop Robin Eames, arranged and attended Wednesday's talks.
An Irish Government spokesperson said there had been a "frank exchange of views".
In a statement, Mr Ahern said the Irish Government was determined to develop its relations with loyalism and unionism.
He reiterated that both governments had made it clear that all ongoing paramilitary activity had to stop.
Mr Ahern referred to what he called the "economic and social circumstances of a number of loyalist areas" and said that measures to support community development in those areas is something that deserved support and required more attention.
Meanwhile, the Progressive Unionist Party has rejected the British and Irish Governments' joint declaration to advance the Northern Ireland political process.
'Unacceptable surrender'
A delegation led by party leader David Ervine expressed its view to the government during a meeting with the Secretary of State, Paul Murphy, on Wednesday.
As a party closely linked to the loyalist Ulster Volunteer Force, the PUP are concerned about the implications of the government's plan to set up a monitoring body to oversee paramilitary activity in the province.
During Wednesday's meeting with Mr Murphy, the party raised concerns about Irish involvement in triggering any complaint to the body.
Mr Ervine argued that it was "an unacceptable surrender of UK sovereignty".
PUP leader David Ervine met Paul Murphy to discuss the joint declaration
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"There is a serious suggestion of removal of at least one item of sovereignty for inclusion to the Irish Government," he said.
"That is unacceptable, it is not for negotiation.
"The British Government are inclined to want monitors almost to abdicate the responsibility that is their own.
"They are the sovereign government and they should behave as a sovereign government and under no circumstances hive off to any other authority the responsibility of ensuring that elements of the law in Northern Ireland are open to UK citizens."
The former deputy leader of the Ulster Unionist Party, Lord Kilclooney, has also expressed his opposition to Irish involvement in the proposed monitoring body.
Lord Kilclooney said the monitoring body proposal would let Dublin "put its toe through the door of the Stormont Assembly".
It is a line of argument very similar to that being advanced by Lagan Valley MP Jeffrey Donaldson.
The anti-Agreement Ulster Unionist has threatened to quit the party unless the governments' proposals are rejected at an emergency meeting of the party's ruling council next
week.
The joint declaration was given to the parties in March in an attempt to move the political process forward in Northern Ireland.
The document included five annexes dealing with security normalisation, policing and justice, human rights and equality, on-the-run paramilitaries and mechanisms to verify and monitor any deal.
Northern Ireland's devolved administration was suspended last October amid allegations of IRA intelligence gathering in the Stormont government.