The court in The Hague stopped short of charging Bashir with genocide, claiming that there was insufficient evidence to support such a claim. The court indicted the 65-year-old Bashir on seven counts for war crimes, crimes against humanity, murder, forcible displacement and other crimes.
"He is suspected of being criminally responsible . . . for intentionally directing attacks against an important part of the civilian population in Darfur, Sudan, murdering, exterminating, raping, torturing and forcibly transferring large numbers of civilians, and pillaging their property," court spokeswoman Laurence Blairon said, according to the Associated Press.
Later Wednesday, the U.N. said Sudan had ordered the expulsion of six to 10 humanitarian groups from Darfur including Oxfam, Solidarities and Mercy Corps, and seized assets.
Sudanese Vice President Ali Osman Mohammed Taha confirmed to the AP that 10 "associations" were asked to stop operating in Sudan for "because they violated laws and regulations."
A press release on the charges says a campaign of attacks on rebel groups that opposed the Khartoum government were a "common plan agreed upon at the highest level of the Government of Sudan by Omar Al-Bashir and other high-ranking Sudanese political and military leaders."
The United Nations has estimated that over the course of six years of conflict in Sudan starting in 2003, around 300,000 people have died and millions have been displaced in Darfur.
ICC prosecutor Luis Moreno-Ocampo initially made a request for the warrant for Bashir's arrest in July 2008. This is the first time since its creation in 2002 that the international court has issued a warrant against a sitting head of state.
"Omar al-Bashir's official capacity as sitting head of state does not exclude his criminal responsibility, nor does it grant him immunity against prosecution before the ICC," Blairon told reporters.
Responding to ICC's warrant, Sudanese presidential adviser Mustafa Osman Ismail told media outlets, "The court is only one mechanism of neo-colonialist policy used by the West against free and independent countries."
Saying he was not surprised by the action of the international court, he told media outlets that "they do not want Sudan to become stable."
The BBC reported that after news of the arrest warrant broke, thousands of protesters took to the streets in support of Bashir in Khartoum.
African and Arab nations have feared an arrest warrant could further destabilize the region. Violence has reportedly risen in Darfur in the months leading up to the ICC decision. Sudanese officials have said they expect Darfur rebels to step up attacks after the court's announcement, Reuters reported.
It is unclear if Bashir will actually be arrested. The court has already issued arrest warrants for Sudanese Humanitarian Affairs Minister Ahmed Haroun and the Janjaweed militia leader Ali Abdul Rahman. Sudan has not responded to either of those warrants.
Al-Bashir denies the war crimes accusations and refuses to deal with the court, and there is currently no international entity to arrest him. The ICC relies on diplomatic pressure for countries to hand over suspects.
Calling the indictment "pretty toothless," Sudan expert Alex de Waal told the BBC that the warrant will be delivered to Sudan's government, which, while it is legally obligated to execute it, would not likely do so.
Reacting to the ICC's warrant, U.S. State Department spokesman Robert Wood said, "The United States believes those who have committed atrocities should be brought to justice."
The announcement received mixed reactions elsewhere. Russian special envoy to Sudan, Mikhail Margelov was quoted by RIA news agency as saying, "The untimely fulfillment of the ICC decision to arrest the President of Sudan will create a dangerous precedent in the system of international relations and could negatively affect the situation both inside Sudan and the overall situation in the region."
There is widespread belief that ICC's arrest warrant may make further peace negotiations with the country difficult. The warrant was issued despite voiced concerns by United Nations diplomats, the African Union, the Arab League, and some humanitarian organizations that said that the warrant could further provoke the Darfur government and renew violence in the region.
According to the New York Times, Salah Gosh, the head of Sudanese intelligence, has been quoted in the Sudanese press as calling for "the amputation of the hands and the slitting of the throats of any person who dares badmouth al-Bashir or support the International Criminal Court's allegations against him."
U.N. Secretary-General Ban Ki-moon called on Khartoum to keep cooperating with all U.N. entities and ensure their safety after the ICC arrest warrant was issued.
"The United Nations will continue to conduct its vital peacekeeping, humanitarian, human rights and development operations and activities in Sudan," the U.N. said in a statement, according to Reuters.