The Sudanese president, Omar al-Bashir, has been charged with war crimes over the conflict in Darfur, becoming the first sitting head of state issued with an arrest warrant by the international criminal court (ICC).

The court, based in The Hague, upheld the request of the chief prosecutor, Luis Moreno-Ocampo, to charge Bashir with war crimes and crimes against humanity. More than 200,000 people have died since 2003 in the country's western Darfur region.

Judges dismissed the prosecution's most contentious charge of genocide. Prosecutors had alleged Bashir tried to wipe out three non-Arab ethnic groups.

Within minutes of the announcement, hundreds of protesters took to the streets in Khartoum, the Sudanese capital.

Mustafa Osman Ismail, an aide to Bashir, described the decision as "neo-colonialism ... They do not want Sudan to become stable."

The ICC spokeswoman, Laurence Blairon, said the indictment, drawn up by three judges, included five counts of crimes against humanity: murder, extermination, forcible transfer, torture and rape. The two counts of war crimes were for directing attacks on the civilian population and pillaging.

Blairon said Bashir was criminally responsible as the head of state and commander of the Sudanese armed forces for the offences during a five-year counter-insurgency campaign against three armed groups in Darfur.

She said all states would be asked to execute the arrest warrant and if Sudan failed to cooperate the matter would be referred to the UN security council.

Human rights groups hailed the ICC decision to pursue Bashir, who is accused of ordering mass murder, rape and torture in Darfur.

"This sends a strong signal that the international community no longer tolerates impunity for grave violations of human rights committed by people in positions of power," said Tawanda Hondora, the deputy director of Amnesty International's Africa programme.

Sudan does not recognise the ICC, and Bashir yesterday said the court could "eat" the arrest warrant, which he described as a western plot to hinder Sudan's development.

Despite his defiance, the court's decision will raise immediate questions over his political future and he will find it difficult to travel abroad without the risk of arrest.

The case is by far the biggest and most controversial that the ICC, which started work as a permanent court in 2002, has taken on.

Bashir, who is 65 and has held power for 20 years, joins the likes of the former Liberian president Charles Taylor and the late Yugoslavian leader Slobodan Milosevic, who were indicted by special international tribunals while still in office.

Both were subsequently forced from power and put on trial in The Hague.

Few independent observers doubt Bashir's large share of responsibility for the humanitarian catastrophe in Darfur.

After the uprising in February 2003 by mainly non-Arab rebels, who complained of marginalisation and neglect, his government armed, trained and financed bands of Arab nomads to attack villages across Darfur, killing, raping and looting as they went. The army provided air and ground support.

Moreno-Ocampo says the strategy caused 35,000 violent deaths, and alleges that Bashir wanted to eliminate the Fur, Marsalit and Zaghawa ethnic groups, whom he deemed supportive of the rebels.

"More than 30 witnesses will [testify] how he [Bashir] managed to control everything, and we have strong evidence of his intention," Moreno-Ocampo said yesterday.

But some Sudan experts were not convinced by the genocide charge, which is normally extremely difficult to prove. Equally contentious was the decision to pursue Bashir while he still heads an unpredictable regime in an unstable country.

The US, UK and France were in favour of the arrest warrant, and hope it may push Sudan's government towards reforms and ending the six-year conflict.

But Arab states and the African Union had pressed for a postponement of the charges to allow Bashir a final chance to end the Darfur conflict while not under duress.

Under the ICC statute, the United Nations can still pass a resolution to defer the prosecution for 12 months, but this seems unlikely given the stance of leading western powers.

Street protests against the ICC decision are expected in Khartoum, but the government has insisted there will be no impact on national policies.

Some observers fear, however, that Bashir will crack down on opposition groups in the coming months if he feels his power is at stake, and that the 2005 peace deal to end the civil war in the south could also be in peril.

The UN, aid agencies and western embassies have made emergency plans in case of violence against foreigners.