Expressing President Thabo Mbeki's regret about the strike on Baghdad, presidential spokesman Bheki Khumalo repeated Pretoria's view that the matter should have been dealt with by the UN, rather than unilaterally by the United States and its allies.
"It is a blow to multi-lateralism," Khumalo said.
In its reaction, the Department of Foreign Affairs said war was not a solution to the world's problems.
The government regretted the start of the war which set an "unfortunate precedent" in dealing with world affairs, spokesman Ronnie Mamoepa said.
"It is also regrettable that the war is occurring outside the mandate of the United Nations Security Council.
"More than ever before, the multilateral system should be used in our response to global challenges, and we call on the United Nations to assert its authority to ensure that military action was conducted in the rules of international humanitarian law."
Mamoepa said the situation was compounded by the fact that progress had been made by UN weapons inspectors in disarming Iraq of weapons of mass destruction. The challenge was for South Africa and civil society to provide humanitarian aid to Iraq, he said, echoing comments by deputy foreign minister Aziz Pahad earlier this week.
Meanwhile, opposition parties urged the South African to remain neutral.
African Christian Democratic Party president Kenneth Meshoe said his party was encouraged that it was still not a full-scale war, in which civilians might lose their lives.
It appeared the initial attack was aimed at trying to force Saddam Hussein out of the country.
"He must think of the interests of his people. The noble thing for Saddam to do is to move out. If I was in his position I would leave," Meshoe said.
South Africa should remain neutral and try to be an "objective mediator".
"We should go back to Saddam and tell him that for the sake of your people you must go into exile," Meshoe said.
In his reaction, Pan Africanist Party leader Dr Stanley Mogoba said the world was receding into the Dark Ages by "returning to a world of war without the sanction of the United Nations or the clear consensus of the nations of the world".
"It is something to be regretted and it will impact very negatively on poor countries."
NNP foreign affairs spokesman Dr Boy Geldenhuys said his party had from the very start believed the US was going to attack unilaterally.
"It is very important for South Africa to stay neutral.
Humanitarian aid must be encouraged but South Africa should at all costs not be seen to support Saddam Hussein," he said.
United Democratic Movement leader Bantu Holomisa said it was unfortunate that a country which was dubbed "the mother of all democracies" had "stooped so low" to try and kill the leader of another nation.
He was referring to the fact that the US cruise missile strike on Baghdad had been described by Washington as a "target of opportunity" aimed at eliminating some of the Iraqi leadership, including Saddam himself.
Holomisa said it was clear that US had wanted a regime change all along, rather than just merely disarming Iraq of weapons of mass destruction.
In his reaction, DA leader Tony Leon said his party's thoughts were with everyone involved in the conflict.
"War is a terrible thing and we regret the crisis couldn't be solved by diplomatic means."
Leon called on South Africa to distance itself from the Iraqi regime and to prepare to offer such humanitarian assistance as it was able to.
He also said South Africa should be prepared to assist in the building of a democratic Iraq once the conflict ended - Sapa
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