Ibrahim, a resident who made it to the Chadian town of Adre, about 27km from El Geneina, told Reuters "all of a sudden the militias came out and sprayed people with gunfire," he said by phone, asking to use only his first name. "We got surprised by thousands of people running back. People were killed, they were trampled."
Ibrahim later found out that eight of his family members had been killed, including his grandmother, and that his mother had been beaten.
Reuters spoke to three witnesses who sustained gunshot wounds as they tried to flee El Geneina, and to more than a dozen witnesses who said they had seen violence on the route from the city. It was not clear how many people had been killed in recent days.
Medical charity MSF said on Monday that some 15,000 people had fled West Darfur over the previous four days, and it said many arrivals reported seeing people shot and killed as they tried to escape El Geneina. MSF also reported rapes.
The violence in El Geneina over the past two months has been driven by militias from Arab nomadic tribes along with members of the Rapid Support Forces (RSF), a military faction engaged in a power struggle with Sudan's army in the capital, Khartoum, witnesses and activists said.
"It was a collective decision of the people of El Geneina to leave", one resident told MSF from Chad. "Most of them fled on foot heading northeast of El Geneina but many of them were killed on this route."
People decided to flee when the state governor of West Darfur was killed on June 14, hours after he accused the RSF and allied militias of "genocide" in a TV interview.
Sultan Saad Bahreldin, leader of the Masalit tribe, the largest bloc of El Geneina residents, said there had been "systematic" killing in recent days.
"The road between El Geneina and Adre has a lot of bodies, no one can count them," he told Al Hadath TV.
One activist who left El Geneina on Sunday told Reuters that Arab militias and the RSF had reinforced their presence in the city since the governor's killing, adding that Arab groups controlled the route to Chad.
The violence in Darfur has increased and taken on a more overtly ethnic nature, with assailants targeting non-Arab residents by their skin color, witnesses said.
There are warning signs of a repeat of the atrocities perpetrated in Darfur after 2003, when "Janjaweed" militias from which the RSF was formed helped the government crush a rebellion by mainly non-Arab groups in Darfur.
RSF leader Mohamed Hamdan Dagalo, known as Hemedti, said on Tuesday his force would investigate events in El Geneina. He accused the army of fomenting violence by arming tribes, while the army has blamed the RSF for the governor's death and other violence in the region.
The war that erupted in April has uprooted more than 2.5 million people, according to U.N. estimates, mainly from the capital and from Darfur, which was already suffering from two decades of conflict and mass displacement. Nearly 600,000 have crossed into neighboring countries, including more than 155,000 who have fled Darfur for Chad.