The strike came the day after the country’s major fuel depots were hit, causing a huge flame just south of the eastern city.
AFP correspondents reported a major explosion at dawn and a surge of smoke across coastal cities.
Two days after the facility’s military base was first attacked with drones, an airport official told AFP.
All flights were grounded at major international ports of entry in the war-torn country, sources added.
Army sources said another drone targeted a major army base in the city centre, but witnesses reported that a nearby hotel was attacked.
The third drone hit a fuel warehouse near Nanko in the dense city centre where the United Nations, aid agencies and hundreds of thousands of displaced people moved from Khartoum.
Witnesses north of the city reported anti-aircraft fire from a military base.
MP/