The fighting in South Sudan has seriously jeopardised the implementation of the 2005 Sudanese peace deal between Sudan and South Sudan, amid fears that it may take more than three years before issues contained in it are addressed.
With the international community backing a three-year interim government as a solution to the conflict, the pending post-referendum issues are now in limbo as the Government of South Sudan is preoccupied with the conflict while Khartoum cannot engage Juba on these issues in the current environment.
The pending post-referendum issues include the demarcated North-South border, the oil-rich Abyei region, security arrangements, wealth-sharing and the issue of citizenship.
Information and Broadcasting Minister, Michael Makuei, who is also the government spokesperson, however told The EastAfrican that while the conflict may have interrupted the implementation slightly, talks are going on since it is a separate issue from the current conflict.
Of great concern is the Co-operation Agreement between the two countries that was signed in Addis Ababa on September 2012, which cannot be implemented in the current state of heightened insecurity and conflict.
While this agreement addressed eight areas of cooperation, among them outstanding issues of security arrangements, the sharing of oil revenues and citizenship, it left out the fluid issues of Abyei and border demarcation.
With a view to ending the tension between the two Sudans, the co-operation agreement recognises the existence of two states, and the two countries agreed to renounce violence in their relations and withdraw support for rebel groups fighting the other state.
It also laid out plans for border demarcation in order to manage the border in a way that recognises the connections between the two peoples now on different sides of it, and that promotes social and economic development along the border.
Prior to the outbreak of the conflict, the African Union High-Level Implementation Panel (AUHIP) led by former South African president Thabo Mbeki, was shuttling between Khartoum and Juba to have the co-operation agreement implemented.
But its implementation has now stalled, and Sudan could easily take advantage of the current conflict to delay the co-operation agreement because Khartoum cannot take seriously negotiations with South Sudan under the prevailing situation.
The issue of Abyei remains the most contentious and may not be solved in the near future given the on-going conflict. The Mbeki group proposed that a binding referendum take place by the end of October last year, without the participation of the Misseriya tribe, now living in Abyei.
This has been accepted by South Sudan, but rejected by Khartoum, as the indigenous Dinka Ngok would be expected to vote for Abyei to be transferred to South Sudan, from where it was moved by the British in 1905.
Khartoum still believes that there are some elements in the South Sudan government that are sympathetic to the rebels, especially the Sudanese People’s Liberation Movement-North (SPLN-N), which is fighting the Sudanese government in Southern Kordofan.
The SPLM-N, and three Darfurian groups the Justice and Equality Movement, two factions of Sudan Liberation Movement led by Abdel Wahid al-Nur and Minni Minnawi sealed an alliance last November 2011 aiming to bring down the Sudanese regime.