Opposition politicians and Irish human rights groups strongly criticised the air strikes, with some accusing President Clinton of acting out of self-interest.
Unease was also displayed by the Government, with the Taoiseach, Mr Ahern, expressing disappointment that the action was "deemed necessary". He called for a peaceful outcome.
The Minister for Foreign Affairs, Mr Andrews, said the use of force against Iraq should be "kept to a minimum" in order to avoid further suffering for the Iraqi people and potentially destabilising consequences in the Middle East.
Speaking to reporters at Iveagh House following discussions with the German Vice-Chancellor and Foreign Minister, Mr Joschka Fischer, Mr Andrews said the Government regretted that it was "not possible for the UNSCOM team of inspectors to complete their work and we are very disappointed that the use of force was deemed necessary".
The Fine Gael leader, Mr John Bruton, said the decision to attack had been taken by the military forces of two countries, without consultation with others. There was a lack of information as to the legal basis for the action.
Describing President Saddam Hussein as "an evil dictator", the Labour leader, Mr Ruairi Quinn, said his continued refusal to allow the UN inspectorate test and inspect military installations was further proof of his malicious intent.
In spite of this, the action taken by the US and Britain was "a disproportionate response to the current situation". It had not been taken with the support of the UN Security Council and had been conducted prior to any real discussion on the UN inspectorate report.
Condemning the bombing, the Democratic Left leader, Mr Proinsias De Rossa, accused the Taoiseach of "weasel words", adding that in reality he supported the action.
The attacks were described as a "cynical act" by the justice and peace organisation, AFrI, which said they had all the hallmarks of "self-preservation" for Mr Clinton.
"If you follow the logic of attacking a country to make the government more democratic and accountable then you should be bombing other countries like Saudi Arabia, but obviously there is more to gain from Clinton's relationship with Saudi Arabia," said the director of AFrI, Mr Joe Murray.
The raids were described as "a disgrace" by Mr Kieran Allen of the No To The Gulf War Campaign, which was founded as a response to the Gulf War in 1991.
"It's quite sick that people have to die just to divert attention from a minor squabble within the US political establishment," he said.
The Green Party MEP, Ms Patricia McKenna, called the attacks "a gross violation of the UN Charter and a serious breach of the principles of international law".
Her party colleague, Mr John Gormley TD, said the bombing of Baghdad was a "cynical attempt" by Mr Clinton to divert attention from the impending impeachment decision against him.
Unsuccessfully attempting to have the Dail sitting suspended to permit a debate on the crisis, the Socialist Party TD, Mr Joe Higgins, called on the Taoiseach to condemn the attack.
"Innocent lives are being sacrificed to save the political hide of the President of the most powerful country on earth," he said.
The Sinn Fein president, Mr Gerry Adams, called for an immediate end to the bombing. "Previous military action against Iraq resulted in the deaths of thousands of innocent people, including women and children, and did not result in the bringing about of a long-term solution to the situation in that region," he said.
The Workers' Party said the attack was an "act of terrorism" which had more to do with the impeachment moves against President Clinton than Iraq's blocking of weapons inspectors.
The director of the Irish section of Amnesty International, Ms Mary Lawlor, said the US and British governments had a duty to protect the lives of civilians.
A spokesman for the Department of Foreign Affairs said no request had been received from the United States to allow American planes to refuel in Ireland en route to the Gulf.