President Salva Kiir has ordered withdrawal of South Sudanese national army soldiers from the border with Sudan.

The decision comes two days after Khartoum agreed to re-negotiate oil transit fees with Juba.

In an official statement seen by The East African, President Kiir also ordered the revival of joint committees between the two countries to implement the cooperation agreement signed between Khartoum and Juba in September 2012.

According to the order, the Southern Sudanese forces will retreat five miles from the border as demarcated in 1956.

''We need to work together with our brothers and sisters in Khartoum to normalise relations,'' President Kiir pointed out.

''I'm confident that my brother president [Omar] Bashir will positively responded to my message, which aims to normalise the relations and to open the common border to allow the flow of trade and transportation for the interests of the two nations,'' he added.

Following South Sudan's independence from Sudan in 2011, a number of issues remain unresolved between the two neighbours. They include border demarcation and even the sharing of debts and assets

Oil transit fees

Khartoum is yet to comment on President Kiir's gesture.

Earlier while speaking in Parliament, Sudan's minister of Finance, Badr Eldien Mahmoud, said that his country had deducted all unpaid fees owed from sale of South Sudanese crude oil. This, Mr Badr said, was to cushion his country after Juba threatened to stop the flow.

South Sudan has been paying a $25 fee to Khartoum per barrel transported.

The current international oil prices are as low as $29 per barrel.

Juba wants a review of the agreement threatening to stop the flow if nothing is done.

South Sudanese ambassador to Khartoum, Mayan Dott, confirmed Saturday that officials from the ministries of oil and finance will hold talks to review the prices.

"We requested Khartoum to sit and renegotiate the oil transit fees due to the decline of the prices and Khartoum has agreed to do that as we enjoy good and understanding relations,'' he stated.

Sudan officials confirmed the development.

“The reality is that the production of oil is down. We are producing about 165,000 barrels a day and on top of that there is the drop in oil prices,” South Sudan’s Foreign Affairs minister Barnaba Marial Benjamin explained.

The east African country receives less than $5 per barrel after transit charges paid to Sudan are deducted and oil companies are paid.

Juba transports her oil for export through a Sudanese pipeline to Port Sudan on the Red Sea.