Tension between Sudan and South Sudan has deepened only two months after normalisation due to claims that Juba is supporting rebels in Southern Kordofan and Blue Nile.

Both sides continue to trade accusation on who is responsible for failing to implement the nine point 2012 co-operation agreement that was meant to improve economic and political ties between the two countries after South Sudan seceded in 2011.

Khartoum has responded by bombing some regions in South Sudan in pursuit of SPLM-N rebels as well as closing the border and stifling the cross-border trade between the two countries. 

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The current bone of contention is the failure by both sides to withdraw eight kilometres from the border as was agreed in January between president Omar al-Bashir and Salva Kiir.

Sudan Ambassador to Kenya Elsadig Abdalla Elias told The EastAfrican that while Sudan has been responding well to the normalisation of relations by starting negotiation on reviewing the economic arrangements between the two countries, South Sudan is yet to withdraw its troops from the border and continue supporting SPLM-N.

“More than 50 days have passed since the statement by President Salva Kiir on the withdrawal of the army, it is yet to be implemented. None of the joint committees has been activated specially the Joint Political and Security Mechanism that is supposed to address the security concerns of the two parties especially the accusations on harbour and support to the rebel movements,” said Mr Elias.

Sudan has also warned that it will start treating as refugees, the 19,608 South Sudanese who entered Sudan after the civil war broke out in December 2013. Till now, Sudan has been treating South Sudanese displaced by war as citizens by allowing them to work and study in the country.

However, South Sudan charge d’Affairs in Kenya, Jimmy Deng said that withdrawal of forces from the border must be gradual and carefully planned because it would leave a gap for other armed groups to continue causing tension between the two countries.

He however denied that Juba is supporting SPLM-N and accused Khartoum of acting on information that has not been verified with the South Sudan government in accordance with the agreement in January to exchange intelligence on disruptive elements from both sides.

“South Sudan currently has no capacity to support any armed group given that we are still dealing with numerous problems such as the civil war, the internally displaced, looming famine and economic problems,” said Mr Deng.

After five years of hostile relations since South Sudan seceded in 2011, the relations between the two countries started thawing in January after President al Bashir agreed to open the border and President Kiir ordered the withdrawal of his forces from the border. President al Bashir had also agreed to renegotiate the payment of $25 oil transmission fee, after Juba complained that it is selling its oil at a loss because of the dipping global oil prices.

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But now tension is escalating between the two countries which experts in region said has been exacerbated by the failure by the Sudan government to implement some articles of the 2005 Comprehensive Peace Agreement (CPA).