Four petrol stations visited by Reuters in Juba, the capital of South Sudan, had run out of petrol while motorists waited in long queues at the few stations that were still open.
"We've run out of fuel," one staff member at a petrol station said, declining to be identified.
"I don't know when new supplies will come and whether we will be able to pay for it."
The dispute over oil payments has stirred serious tensions between the two former civil war foes, escalating into border clashes that risk pushing the two neighbors into a full-blown war.
The Sudanese army said on Saturday it was fighting South Sudan's forces in the disputed Heglig region just a few kilometers (miles) from a key oilfield, although South Sudan denied the claim.
On Sunday, Khartoum warned it would not negotiate with Juba until South Sudan withdrew all its forces from the area. A South Sudanese government spokesman in turn accused the north of bombing Heglig's oil facilities "to rubble"
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