Newspaper reports that a serving Cabinet member received an £80,000 payment were rejected by the Minister for Foreign Affairs, Mr Cowen, yesterday.
He said speculation on these issues was "without foundation".
"I know nothing about it. I don't know anyone else that knows anything about it and I really don't think it serves the purposes here," Mr Cowen said. He was speaking at a Nice campaign poster launch, in his new role of director of Fianna Fáil's Nice campaign.
"The tribunal have issued their report. They deal with the findings and the facts and if anyone has any evidence of any problems, the tribunals are there to deal with it and they have the powers to deal with it," the Minister said.
The Government was trying to get on with its job of running the country, he added. "And those who have any problems in relation to any other issue, we say 'co-operate with the tribunal and deal with it'. But we have no basis for any of this speculation at the moment. We don't know what that's about."
Asked if he could condemn Mr Ray Burke, Mr Cowen said Fianna Fáil had always said the public's trust should never be breached. He said the party accepted and welcomed Mr Justice Feargus Flood's findings.
"So there is no question of ambiguity as far as our party is concerned. We co-operate fully. Nothing was done with our knowledge, with our agreement, with our consent as a party. And if there are any breaches of fundamental trust, they have to be dealt with and will be dealt with.
"So the idea, or the attempt to suggest that Fianna Fáil are in any way ambivalent about this matter, I'm afraid, doesn't stand up to scrutiny."
He said he hoped "whatever further necessary measures have to be taken will be taken in a way which won't be prejudicial to the outcome."
Not prejudicing any action taken by other agencies was "a very important consideration", Mr Cowen said.
"We must get on with our work. We are the Government," he said. "Let's get on with that business and let the tribunal get on with their business."
The Minister for Foreign Affairs had earlier stressed that a Yes vote would give "the strongest ever protection" to Ireland's neutrality.
"A new declaration signed by all 15 EU members spells out very clearly that our neutrality is fully protected now and into the future," Mr Cowen said.
