Landlocked southern Sudan becomes an independent state in July as part of a 2005 comprehensive peace agreement that ended a civil war.
The 2005 deal outlines equal revenue sharing from oil pumped from southern Sudan.
"Either we continue the split or we take our right from any oil that passes through our land here," Sudanese President Omar Bashir was quoted by Bloomberg News as saying. "If you don't want either of the two options, we will shut the pipeline."
South Sudan takes control of 75 percent of the united country's oil production of 490,000 barrels per day when it gains independence.
Both sides agreed in May that South Sudan will pay the government in Khartoum pipeline and export related fees. Sudanese Oil Minister Lual Deng, a member of the south's ruling Sudan People's Liberation Movement, said the fees must be "reasonable" or Juba would start looking for other export options.