The attackers violently assaulted a team of 18 people working for the global aid organisation on Thursday as they attempted to bring supplies to the Turkish Hospital in southern Khartoum, the aid group said in a statement on Friday.
Reuters could not independently confirm the incident, and representatives for Sudan's health ministry did not immediately respond to a request for comment. It was unclear which if any rivalling faction may have been behind the alleged attack.
"After arguing about the reasons for MSF's presence, the armed men aggressively assaulted the MSF team, physically beating and whipping them," the charity, also known as Medecins Sans Frontieres (MSF), wrote.
"They detained the driver of an MSF vehicle, threatened his life before releasing him, and stole the vehicle."
Fighting broke out April 15 between the Sudanese military and the Rapid Support Forces paramilitary group, driving civilians out of the wider capital region and triggering ethnically motivated attacks in the western Darfur region.
Those who have not fled the African country have faced a severe humanitarian crisis, with scarce access to clean water, medical care and other essential services as aid groups scramble to help.
MSF said the incident jeopardised its activities at the hospital, one of only two that remain open in southern Khartoum.
"If an incident like this happens again, and if our ability to move supplies continues to be obstructed, then, regrettably, our presence in the Turkish Hospital will soon become untenable," said Christophe Garnier, MSF's emergency manager for Sudan, adding that minimum safety guarantees were needed to continue its work.
Regional and international mediation efforts have so far failed to end the fighting, and UN officials fear Sudan could slide into civil war.
