Mr. Bashir is already shunned by numerous leaders from countries who recognize the court’s jurisdiction  111 countries adhere to it  and while the leaders of many Arab and some African countries continue to meet with him, others have warded off visits by warning that as court members they are legally bound to arrest him. As a result, Mr. Bashir has avoided a number of conferences and celebrations in Africa, Europe and the United States in the last two years.

Image President Omar Hassan al-Bashir of Sudan, during his inauguration in Khartoum in May. His re-election was marred by allegations of fraud. Credit... Philip Dhil/European Pressphoto Agency

It was not clear when the arrest warrant was served. The court disclosed the decision on Monday afternoon by posting it on the court’s Web site. The order said there were reasonable grounds to believe that security forces and militia under Mr. Bashir’s command had attacked the Fur, Masalit and Zaghawa ethnic groups of Darfur in ways that “were calculated to bring about the physical destruction of part of those ethnic groups.” It cited torture, rape, the poisoning of water, expulsions and killings as part of what it called “the genocidal policy.”

The judges’ new arrest warrant came as a vindication for the prosecution, which has spent more than a year seeking genocide charges against Mr. Bashir. Judges in the court, the first permanent international criminal court, which opened its doors in 2002, must endorse the prosecution’s accusations. It is the judges who then call for an arrest, an extra step in the rules to safeguard against a possible rogue prosecutor.

Last year, the judges turned down the prosecution’s request to charge the president with genocide, saying that the evidence presented was insufficient. But an appeals chamber called this “an error of law,” because the judges had sought far higher standards of proof than were required to order an arrest, and it asked them re-examine the application.