Dozens of buses queued for fuel on Saturday at Khartoum-area petrol stations but an oil ministry official said there was no connection with fighting in the oil fields of South Sudan.
Between 35 to 50 minibuses, which move passengers throughout the Sudanese capital, were seen 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.
Another, Omar Abbas, said he drove to five petrol stations until he finally found one where he could buy diesel.
"Now I've been waiting for an hour, and I've got more waiting ahead of me," he said.
Petrol station staff said they had not received their regular supply of diesel.
"We got only half of it," said a worker at one Khartoum station. "We don't know why."
At another outlet, an employee said none of the allotment had arrived.
Both workers declined to be named.
The shortage was only temporary and had absolutely no connection with fighting by rival army factions in neighbouring South Sudan, Hisham Taj Elsir, general manager of supply and petroleum trade at Sudan's oil ministry, told AFP.
"We have enough supply. No problem," Elsir said, blaming the distribution company which on Friday withdrew only one-third of the 1,800 tonnes allocated for Saturday's consumption.
Customers who heard about a shortage and tried to hoard fuel added to the problem, he said.
Sudan's Information Minister Ahmed Bilal Osman on Friday expressed concern over the fate of economically vital oil flows from South Sudan as fighting between rival army factions spreads there.
"Definitely one of the targets of the two powers, will (be to) try to take over the oil fields," perhaps as a way to improve their bargaining position, he told AFP.
But "so far, there is no effect" on oil moving through Sudan, Osman said.
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.
Elsir said all the South Sudanese oil passing through Sudan's infrastructure is sold abroad.
"We don't take from them any oil," he said, adding Sudan's own production of about 130,000 barrels per day provides more than enough for domestic gasoline consumption.
"We have a surplus," he said.
Diesel, however, was supplemented by imports and another ship arrived with more of the fuel on Saturday, he said.
South Sudan's army spokesman Philip Aguer said on Saturday that 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.
At least five South Sudanese workers were killed late on Wednesday after unidentified attackers stormed their compound in Unity state, operated by the Greater Nile Petroleum Operating Co., a senior executive with the firm said.