The Minister for Foreign Affairs has assured Ulster Unionists that the new arrangements to keep the North/South implementation bodies in operation are purely temporary and will lapse if the North's political institutions are suspended for a lengthy period.
Mr Cowen made his comments at a meeting last night with an Ulster Unionist delegation who travelled to Dublin to express opposition to what they feared was an attempt by the governments to continue to develop the North/South Ministerial Council despite the suspension of the political institutions.
The UUP leader and his colleagues have expressed anger in recent days at what they saw as an attempt to circumvent the suspension of the institutions.
However, Mr Cowen told reporters after last night's meeting that legislation introduced by the Government three weeks ago was purely to ensure the essential care and management of the six bodies in the short term. If the suspension of the institutions looked like becoming long term, the arrangements would lapse.
This would threaten the continued operation of the institutions, which employ 700 people from North and South. The bodies are Tourism Ireland, Waterways Ireland, Intertrade Ireland, the Food Safety Authority, the Foyle and Carlingford Fisheries Commission and a body promoting the Irish and Scots-Gaelic languages.
Last night's meeting appeared to take some of the heat out of the issue but the UUP deputy leader, Sir Reg Empey, said afterwards that "matters are not resolved". Mr Cowen undertook to reflect on the UUP concerns and consult with the Northern Secretary, Mr Paul Murphy. Sir Reg said he hoped the Government now had a better understanding of the UUP's position.
Both he and Mr Cowen said this matter was a distraction from the attempt to have the North's political institutions restored.
Mr Cowen said he wanted to "impress on everyone that the Government simply wants to ensure that the care and management of these bodies is allowed to continue. Temporary and remedial are the buzz words here. As soon as we get the institutions restored this issue goes away".
The UUP delegation also complained that they were not consulted in advance of the Government passing the legislation needed to allow for these arrangements. Had they been consulted, they would have raised their objections then.
However, the Dublin view is that the British government was fully aware of what was happening, and that it believed London would have informed the unionists. Mr Cowen is understood to have pointed out that the British had also assumed powers to continue with the North/South bodies.
Minister of State, Mr Tom Kitt, accompanied Mr Cowen at last night's meeting. Sir Reg Empey was accompanied by former Stormont Arts Minister, Mr Michael McGimpsey, and advisor to Mr Trimble, Mr David McNarry.