South Sudan said there were problems with getting its oil to international markets because it suspected Sudan shut a cross-border pipeline.
South Sudan has controlled the bulk of the region's oil reserves since it gained independence from Sudan in 2011. Sudan controls the export pipelines, however, and disputes over transit fees prompted the South Sudanese government to halt oil production last year.
Sudan confirmed that it was getting some oil from South Sudan after officials agreed in April to resume bilateral cooperation as part of agreements reached last year.
South Sudan Foreign Ministry spokesman Mawien Makol Arik was quoted by the New Vision newspaper in Uganda as saying there was "a problem" with oil on the other side of the border.
"But we suspect it is political," he said. "We suspect that Sudan has shut down the oil pipeline."
Sudan denied the allegations.
Conflicts in 2012 in the oil-rich area of Heglig, near the shared border, nearly pushed both countries to war. South Sudan relies heavily on oil for government revenue.