South Sudan accused Khartoum of trying to charge too much for use of the northern pipeline and said it might shut it down, signalling a further rise in tension as both sides argue over dividing oil revenues.
The South took 75 percent of the country's oil production of 500,000 barrels of oil when it became independent on July 9 as part of a 2005 peace deal that ended decades of civil war with the north.
But it depends on the North to use its refineries and the only cross-border pipeline to the Red Sea outlet of Port Sudan to sell the oil, the lifeline of both economies.
"The amount of money Khartoum wants us to pay is unreasonable," David Loro Gubek, under-secretary at South Sudan ministry of energy and mining, told Reuters in an interview.
For use of its oil facilities, North Sudan has demanded fees worth a third of the export value of landlocked South Sudan. Both sides have so far failed to agree on usage fees in a row that could disrupt supplies from one of Africa's largest producers.