Bashir said he would "completely close the pipeline" that carries oil from South Sudan to ports on Sudan's Red Sea coast.
He was speaking at a ceremony after the army recaptured Abu Kershola town in the far north of oil-rich South Kordofan, which rebels seized a month ago.
"We warn the government in the South that if they provide any assistance to the Sudan People's Liberation Movement-North (SPLM-N) or to the rebels in Darfur, we will completely close the pipeline," said Bashir.
In March Sudan and South Sudan, which split from Khartoum in July 2011, signed detailed timetables to resume the flow of South Sudan oil through a major pipeline in the north that runs to a port on the Red Sea, and eight other pacts to normalise relations.
Bashir said yesterday that all of the nine agreements must be respected.
"Failure to abide by any agreement will nullify the nine accords," he said.
Bashir's remarks come less than a month after the Khartoum government announced that South Sudanese petroleum had returned to Sudan's main Heglig facility.
The pipeline will carry oil that will bring billions of dollars in revenue to both impoverished nations once exports resume.
But Khartoum accuses South Sudan of backing rebels fighting in South Kordofan and Blue Nile states as well as in Darfur -- claims which Juba denies.
Bashir's remarks were delivered at a ceremony to celebrate the army taking back Abu Kershola, a town which rebels of the Sudan Revolutionary Front coalition seized on April 27 during attacks on several nearby areas in South Kordofan.
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