Dozens of buses have queued for fuel at Khartoum-area petrol stations but it was unclear if the diesel shortage was linked to fighting in the oil fields of South Sudan.
An AFP reporter saw between 35 and 50 minibuses, which move passengers throughout the Sudanese capital, lined up to buy diesel.
"I have been here with my bus for three hours waiting to get fuel," bus driver Ahmed Omer told AFP.
There were no lines for passenger cars buying petrol.
Sudan's Information Minister Ahmed Bilal Osman on Friday expressed concern over the fate of vital oil flows from South Sudan as fighting between rival army factions spreads there.
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But "so far, there is no effect" on oil moving through Sudan, Osman said on Friday.
Sudan's cash-starved economy is to receive an estimated $1.5 billion (1.1 billion euros) in fees from South Sudan next year for moving crude through northern pipelines for export.
South Sudan's army spokesman Philip Aguer said Saturday contact had been lost with an army commander in oil-producing Unity state, across the border from Sudan.
Aguer said there were reports the commander had joined the forces of fugitive former vice-president Riek Machar, whose troops have been fighting for six days against those loyal to President Salva Kiir.
