"Forty civilians have been killed in an air strike that hit two markets and a number of the city's neighborhoods," the medical source told AFP from a hospital in Nyala, the capital of South Darfur. The source asked for anonymity out of security concerns, France 24.
Witnesses in the area had earlier reported air strikes falling on two markets and causing civilian casualties in Sudan's second-biggest city, where fighting intensified last month.
The vast region of Darfur – the size of France and home to a quarter of Sudan's population – has seen some of the worst fighting in the five-month war between the regular army and the paramilitary Rapid Support Forces, led by Burhan's former deputy Mohamed Hamdan Daglo.
Since April 15, nearly 7,500 people have been killed, according to a conservative estimate from the Armed Conflict Location & Event Data Project.
Wednesday's attack came a day after a medical source reported 17 civilians killed in Khartoum's sister city of Omdurman. Witnesses described the attack as RSF shelling.
On Sunday, at least 51 people were killed and dozens wounded in air strikes on southern Khartoum, according to United Nations human rights chief Volker Turk.
The armed forces control the skies over Khartoum, while RSF fighters continue to dominate the city's streets.
The war between Sudan's army, led by Gen Abdel Fattah Al Burhan, and the Rapid Support Forces, under the control of Gen Mohamed Dagalo, has raged on since April 15.
The conflict, which started in the capital Khartoum, has spread to the western region of Darfur, Kordofan and Jazira state, killing thousands and forcing millions to flee their homes.