The violence in El Geneina in 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.
A large number of people tried to seek protection near the army headquarters in El Geneina on June 14 but were blocked, said Ibrahim, a resident who made it to the Chadian town of Adre, about 27 kilometres from El Geneina.
"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."
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 some 15,000 people had fled West Darfur in the previous four days.
It said many arrivals reported seeing people shot and killed as they tried to escape El Geneina.
MSF also reported rapes.
"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, Ibrahim said.
Ibrahim later found out eight of his family members had been killed, including his grandmother, and his mother had been beaten.
The war that erupted in April has uprooted more than 2.5 million people, according to United Nations estimates, mainly from the capital and from Darfur, which was already suffering from two decades of conflict and mass displacement.
Almost 600,000 have crossed into neighbouring countries, including more than 155,000 who have fled Darfur for Chad.
A 72-hour ceasefire, brokered by Saudi Arabia and the US, due to expire early on Wednesday morning, has brought a lull in fighting in Khartoum although residents report looting has spread and the army said the RSF had caused a huge fire at the intelligence headquarters late on Tuesday.
The RSF said the army was responsible for targeting the building, which is in an area near the defence ministry, army headquarters and airport that both sides claim to control.
The violence in Darfur has increased and taken on a more overtly ethnic nature, with assailants targeting non-Arab residents by their skin colour, 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.
More than 300,000 people were killed and 2.5 million displaced, according to UN estimates.
