The army said Khalil Ibrahim, who led the Darfur-based Justice and Equality Movement (JEM) was killed during a military offensive in North Kordofan state to retaliate for a deadly rebel attack there on Saturday.
JEM is the most organised and effective military force in Darfur, the western region besieged by conflict since 2003. An army statement said Ibrahim and several allies were killed in Wad Banda, about 440 miles west of Khartoum in the North Kordofan region, which borders Darfur.
“The army cut all paths for the group as it was retreating and trying to cross into South Sudan to reorganise it forces,” said Sudanese army spokesman Colonel Sawarmy Khaled. “Our gallant armed forces were able to kill rebel Khalil Ibrahim along with some of his associates.”
One source close to the rebels said he was “pretty sure” reports of his death, which was not independently verified, were true.
JEM did not join a peace deal signed last year between other Darfur rebel groups and Sudanese president Omar al-Bashir’s government in Khartoum.
Ibrahim’s death would be a serious blow to JEM, which has on several occasions threatened to bring down Mr al-Bashir’s regime in Khartoum.
Attacks launched by the group include one on the capital, Khartoum in 2008.
More than 220 people were killed when the rebels reached Umdurman, across the River Nile from the presidential palace. Government troops forced them back after heavy fighting.
On Saturday, JEM announced it was planning a fresh attack on the capital.
The Sudanese government has also claimed the group had offered assistance to former Libyan leader Muammar al-Gaddafi during his attempts to hold on to power. Gaddafi had offered them financial and military aid as well as a safe haven in the capital Tripoli, some commentators have claimed. Ibrahim is believed to have returned to Sudan after the fall of Tripoli earlier this year.
Darfur has been in turmoil since 2003, when ethnic African rebels, accusing the Arab-dominated Sudanese government of discrimination, took up arms against it. The Khartoum government is accused of retaliating by unleashing Arab militias on civilians, which it denies. The UN estimates 300,000 people died and 2.7 million have been displaced during the crisis.
The International Criminal Court in the Hague has issued an international arrest warrant for Mr al-Bashir for his alleged role in crimes against humanity in Darfur.
Fighting in Wad Banda had flared up in the past few days. On Saturday, the Sudanese army said Darfur rebels attacked three locations in neighbouring North Kordofan, killing an unspecified number of civilians. JEM has not claimed responsibility for the attack. A security officer with the United Nations Mission in Darfur said JEM mostly operates out of North Kordofan state and no longer has an official presence in Darfur.