Sudan immediately rejected the decision of the three-judge panel describing it as part of a "neo-colonialist" plan.
"They do not want Sudan ... to become stable," Mustafa Osman Ismail, an adviser to the Sudanese president, said.
"The court is only one mechanism of neo-colonialist policy used by the West against free and independent countries."
Hundreds of Sudanese took to the streets of the capital, Khartoum, to protest against the warrant. The country's ruling party, the National Congress party, said a "million man march" was planned for Thursday.
'Directing attacks'
Laurence Blairon, a spokeswoman for the ICC, said al-Bashir was accused of "intentionally directing attacks against an important part of the civilian population of Sudan; murdering, raping, torturing, forcibly transferring large numbers of the population and pillaging their property".
"Omar al-Bashir's official capacity as a sitting head of state does not exclude his criminal responsibility, nor does it grant him immunity from prosecution," she said.
He is the first sitting head of state to be ordered to face the tribunal since it began work in 2002.
Luis Moreno-Ocampo, the ICC prosecutor who called for an arrest warrant to be issued in July last year, said that al-Bashir must be arrested "to stop him from destroying evidence and committing new crimes".
"It is time to protect the victims, to stop bombing civilians, to stop rapes, to stop the crimes," he said after the judges' decision was announced.
Moreno-Ocampo says he has strong evidence that al-Bashir personally instructed his forces to annihilate three ethnic groups - the Fur, the Masalit and the Zaghawa - and says about 2.5 million people have been victimised by his actions.
The panel decided there was insufficient evidence to support additional charges of genocide requested by the prosecution.
The UN says up to 300,000 people have died since conflict broke out in the western Darfur region in 2003, when ethnic minority fighters took up arms against Sudan's Arab-dominated administration for a greater share of resources and power.
ICC powers
The ICC has no powers to enforce its own arrest warrants, but suspects can be arrested on the territory of states which have signed up to the court's founding Rome Statute.
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| Al-Bashir has refused to recognise the authority of the ICC [AFP] |
"The court doesn't have a police force and therefore relies on those countries who have signed up to the court ... to use their power and their police forces to make the arrest," Stuart Alford, of the war crimes committee at the International Bar Association, said.
"As long as he is president and retains power within his borders ... it will be practically difficult to enforce his arrest," he told Al Jazeera.
Moreno-Ocampo said Sudan was obliged under international law to carry out the arrest on its territory.
"If it does not, the UN Security Council will need to ensure compliance," he said.
But Abdel Basit Sabdarat, Sudan's justice minister, said on Wednesday that Khartoum would not co-operate with the ICC.
"It has no jurisdiction, it is a political decision," he said.
The president has refused to acknowledge the authority of the court and, ahead of the announcement, he told reporters that any attempt to prosecute him would have "no value".
Licences revoked
Sudan revoked the operating licences of up to 10 aid agencies in the country on Wednesday, the UN said.
Alun McDonald, a spokesman for Oxfam, one of the agencies to have its licence revoked, said it was "going to have a devastating effect on hundreds of thousands of people".
"We work with 600,000 people in north Sudan, 400,000 of them in Darfur. It is of the utmost importance the government agrees to let us continue that work."
Al Jazeera's Mohammed Adow, reporting from Juba in southern Sudan, said that the issuing of the warrant could harm the stability of Africa's largest nation.
"No doubt this is a decision that is going to have wide-reaching ramifications on Sudan's stability," he said. "Definitely it is going to embolden the rebels in Darfur.
"Also at stake are agreements that have been signed across the country with various rebels, and chief among them the comprehensive peace agreement that has given autonomy to the south."
The Khartoum government signed a deal with rebel forces in the south in 2005 to end 21 years of fighting.
China, the African Union and the Arab League have suggested an indictment could worsen the Darfur conflict and destabilise the entire region.