The Dáil meets in emergency session this morning to debate the war in Iraq.
The Government will table a motion on the crisis that will be strongly criticised by Opposition parties, who claim neutrality has been abandoned by the Coalition.
In a two-hour meeting yesterday, ministers agreed the motion wording from the Minister for Foreign Affairs, Mr Cowen.
The motion "recalls the long-standing arrangements" covering Shannon and US military overflights, and "supports" the Government's decision to continue those arrangements.
Mr Cowen said this morning he "deeply regretted" that negotiations had failed and attacks on Iraq had been launched.
"Of course we deplore the fact that we are now in a situation where military action is being taken," Mr Cowen told RTÉ. "We recognise that within the Security Council there was a failure to act collectively, to be able to proceed with an agreed way forward.
"And we are stating clearly, consistent with our position set out back in October under Resolution 1441, that on that basis we can't participate in relation to this military action," he said. "I think it is clear nobody welcomes the fact that military action is taking place."
Last night Labour accused the Government of abandoning the principles of international law. The party's foreign affairs spokesman, Mr Michael D. Higgins, said the Republic would be the only state in the EU to assist in a pre-emptive attack by the US.
"Political expediency and commercial interests have been allowed to take precedence over human life and the principles of international law," he said."Facilities that may quite properly be made available to a friendly country in a time of peace are not appropriate during a time of war, especially when that war is being launched in defiance of the UN Charter."
Fine Gael said the Government motion did not uphold the importance of the UN. Its foreign affairs spokesman, Mr Gay Mitchell, said: "We could not be armed so poorly were it not for the collective security that the UN provides." Mr Mitchell said the Dáil should be prepared to say it opposed the war and could not support it or participate in it.
The Greens said the Government's position was "spineless and craven", adding that the motion was much worse than expected. The party's foreign affairs spokesman, Mr John Gormley, said the Government was critical of Iraq and supportive of the United States.
Sinn Féin's foreign affairs spokesman, Mr Aengus Ó Snodaigh, said Mr Ahern's position was "unprincipled and unjustified", while the Socialist Party leader, Mr Joe Higgins, said the Government motion revealed "monumental hypocrisy and utter moral delinquency".