Khartoum - The government of Southern Sudan has re-iterated that it does not support insurgents in the north after Sudan's president Omar al-Bashir ordered that the flow of oil should be stopped.
Experts said on Sunday however that the process could take weeks.
Bashir on Saturday said petroleum companies working in South Sudan would be informed about "shutting down the pipeline" from Sunday, a report said.
The order came after Bashir again warned the South over backing rebels, who analysts say humiliated the authorities with recent attacks.
South Sudan's government in Juba denied the claims.
"I think if you do it properly it would take 45 days to stop the oil without causing damage", said an expert.
"It's not like opening and closing a water tap."
This will be the second closure of South Sudan's oil wells and the Sudanese pipeline system in about 18 months.
Production had only resumed in early April after the two countries agreed on detailed timetables to normalise relations after intermittent border clashes.Pipeline
The South stopped its crude production in early 2012 after accusing Khartoum of theft in a dispute over export fees.
The previous shutdown "went very well", the expert said, adding Sudan's oil ministry had enough experience to safely close the system and its pipeline running 1 500km to the Port Sudan terminal.
The expert said thousands of wells on the South Sudanese side would have to be shut down one by one and the pipeline flushed.
"You need to get rid of the oil somewhere," the expert said.
"If they do not do that properly the oil will gel.
"It's not easy to reverse it to liquid again."
The expert was not sure what point the oil had reached in the pipeline but said "it should be close to Port Sudan".
Bashir warned on May 27 that he would block the oil if the South's government provided assistance to rebels fighting in South Kordofan and Blue Nile states, or in the Darfur region.
Khartoum has long accused South Sudan of supporting rebels in the north, a complaint which for months held up implementation of the oil and security pacts.
Follow Fin24 on Twitter, Facebook, Google+ and Pinterest.