The team was transporting medical supplies to the Turkish Hospital in southern Khartoum Thursday when the armed men attacked them, "physically beating and whipping them," the aid organization said in a statement.
The men also threatened to kill an MSF driver before releasing him and stealing the vehicle.
"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. Speaking to VOA, Garnier denounced the attack as "unacceptable" and "very concerning."
He said the armed men who attacked the aid workers appeared drunk, and it wasn't apparent which group they belonged to.
Sudan's army and the Rapid Support Forces have been battling for control of the country since April when fighting broke out between rival generals.
Sudanese authorities say over 3,000 people have been killed in the conflict.
Over 3 million people have been displaced, according to the United Nations, with the humanitarian situation worsening.
"Civilians and humanitarians shouldn't be involved in the conflict," Garnier told VOA, urging all sides of the conflict to guarantee the safety of aid workers and their ensure access to vulnerable populations.
The Turkish Hospital is one of few hospitals still administering medical care in the country.
VOA's Carol Van Dam contributed to this report.