Evidence presented by prosecutors showed Bashir "masterminded and implemented a plan to destroy in substantial part" three tribal groups in Darfur because of their ethnicity, the ICC said in a statement.
The court's prosecutor for Darfur, Luis Moreno-Ocampo, will now ask a panel of ICC judges to issue an arrest warrant for the Sudanese president, who has repeatedly refused to recognise the court's jurisdiction. The process could take months.
Although Bashir faces three counts of genocide, five of crimes against humanity and two of murder, there is very little prospect of him facing trial in The Hague.
His country has not handed over two nationals previously indicted for alleged abuses in Darfur, a government minister and a militia leader.
"We don't recognise whatever comes out from the ICC, to us it is non-existent," a spokesman for Sudan's foreign ministry, Ali al-Sadig, told Reuters.
There are also concerns that reaction in Sudan over any plans to arrest Bashir could complicate humanitarian efforts to help the millions affected by the conflict or imperil UN-African Union peacekeepers in Darfur.
Tanzania, whose president chairs the African Union, called today for the court to call a halt to the process.
"We would like ICC to suspend its decision to seek Bashir's arrest for a moment until we sort out the primary problems in Darfur and southern Sudan," the country's foreign minister, Bernard Membe, said.
In a brief statement, the UN secretary general, Ban Ki-moon, said he expected Sudan to "ensure the safety and security of all United Nations personnel and property".
More than 200,000 people have been killed and nearly 2.5 million have been made homeless since a revolt broke out in Darfur, a vast, mainly arid province in western Sudan in 2003.
Bashir's regime is accused of deliberately organising Arab Janjaweed militias to attack Darfur's black African civilian population, something it denies.
The ICC statement of charges says Bashir's policy amounted to genocide because those forced into refugee camps had suffered both regular attacks from militias and a deliberate policy of persecution and hunger.
"Bashir organised the destitution, insecurity and harassment of the survivors. He did not need bullets. He used other weapons: rapes, hunger, and fear - as efficient, but silent," Moreno-Ocampo said in the ICC statement.
Bashir was directly responsible, the prosecutor added: "[He] is the president. He is the commander-in-chief. Those are not just formal words. He used the whole state apparatus. He used the army; he enrolled the militia/Janjaweed. They all report to him. They all obey him. His control is absolute."
Speaking before he unveiled the charges, Moreno-Ocampo said he was not swayed by the possibility that the ICC's decision could prompt a violent reaction.
"The genocide is ongoing," he told the Associated Press. "Seventy-year-old women, six-year-old girls are raped," he said: "massive rapes, gang-rapes, rapes in front of the parents."
Drawing a direct comparison with the policies of Nazi Germany, the prosecutor said the international community needed to take stronger action.
"These 2.5 million people are in camps. They [Bashir's forces] don't need gas chambers because the desert will kill them," he said.
"The international community failed in the past, failed to stop Rwanda genocide, failed to stop Balkans crimes. So this time the new thing is, there is a court, an independent court ... who is saying, 'This is a genocide."'
Bashir's National Congress yesterday warned of "more violence and blood" in Darfur if an arrest warrant were issued, state TV reported.
Hundreds of people demonstrated in support of the president outside a cabinet meeting called by Bashir to discuss a response, waving signs condemning the ICC and Moreno-Ocampo.
Last year, Moreno-Ocampo issued arrest warrants against a Sudanese government minister and a commander of the government-backed Janjaweed militia over 51 counts of war crimes and crimes against humanity, including murder, rape and forced expulsions.
However, the minister, Ahmad Muhammad Harun, remains in the government, in charge of humanitarian aid in Darfur.
This is the first time the ICC, a permanent court to deal with war crimes, has levied war crimes charges against a head of state. In the past, specific war crimes tribunals have been convened to charge the former Serbian leader Slobodan Milosevic and Charles Taylor of Liberia.
© 2008 The Guardian