The warrants were a crucial step toward bringing atrocities in the Sudanese region before a panel of international judges in The Hague. However, Sudanese authorities have in the past refused to arrest and turn over suspects to the court and it was unclear whether either suspect would surrender.
"The judges have issued arrest warrants. As the territorial state, the government of the Sudan has a legal duty to arrest Ahmad Harun and Ali Kushayb," Prosecutor Luis Moreno-Ocampo said in a statement. "This is the International Criminal Court's decision, and the government has to respect it."
In February, Moreno-Ocampo named Harun, Sudan's minister for humanitarian affairs, and Kushayb, a janjaweed militia leader, as suspects in a total of 51 counts of war crimes and crimes against humanity including the murder, rape, torture and persecution of civilians in Darfur.
Moreno-Ocampo said the issuing of warrants underscored the strength of his case.
"We completed an investigation under very difficult circumstances, from outside Darfur, and without exposing any of our witnesses," he said. "We transformed their stories into evidence, and now the judges have confirmed the strength of that evidence."
Harun is currently in the Sudanese capital, Khartoum.
Justice Minister Mohamed Ali al-Mardi has said the Sudanese authorities conducted their own investigation into Harun's activities and found "not a speck of evidence" against him.
The Sudanese government says it has arrested Kushayb pending an internal investigation, but several witnesses told The Associated Press in Darfur that he was freely traveling from one Darfur town to another under police protection.
Kushayb has denied leading a group of janjaweed militias in attacks on civilians in Darfur. He told the pro-Arab, pro-Islamist Al Intibaha newspaper that he "did not kill any innocent people" and "did not cause the displacement of any people."
The atrocities allegedly were committed during attacks on four towns and villages in West Darfur between August 2003 and March 2004. Harun and Kushayb were part of conspiracy to "persecute civilians they associated with rebels," Moreno-Ocampo alleged following a 20-month investigation ordered by the U.N. Security Council in 2005.
Their methods were "indiscriminate attacks against the civilian population, murder, rape, inhumane acts, cruel treatment, unlawful imprisonment, pillaging, forcible transfer and destruction of property," according to a 94-page prosecution document outlining the allegations and seeking a judicial order for the men to be handed over to the Hague-based court.
More than 200,000 people have been killed and 2.5 million made refugees in Darfur since 2003, when ethnic African rebels took up arms against the Arab-led Sudanese government, accusing it of neglect and discrimination. The government is accused of arming the janjaweed as a counterinsurgency tactic, and the militiamen are blamed for widespread rapes and killings against Darfur civilians.
Although Sudan does not recognize the court's jurisdiction, the 2005 U.N. Security Council resolution that triggered the Darfur investigation calls on Khartoum and all other groups in the conflict to cooperate fully with the court and the prosecutor.