The impact of the Sudanese government's decision to expel 13 international aid organizations will be felt most immediately in Darfur, where the U.N. says those organizations provided half of the humanitarian operations, and where rebel groups have said they will not continue negotiations with the government. But observers also fear that the move could cause a deterioration in relations between the north and south, where a fragile peace agreement has been in place since 2005.
Since 2005, Sudan's ruling National Congress Party has been sharing power in the national government with the Sudan People's Liberation Movement, or SPLM, former rebels who now control a semi-autonomous region in the South. Cabinet positions, oil revenues, and other resources are split between the two sides.
But when the Sudanese government earlier this month announced the expulsion of 13 international aid organizations for passing information to the International Criminal Court, which had just issued a warrant for the arrest of President Omar al-Bashir, the SPLM was not consulted, according to Southern Sudan's information minister, Gabriel Changson Chang.
"The decision to discontinue the activities of NGOs in Darfur or in Northern Sudan was arrived at without coordinating with the government of southern Sudan, so we are not party to that and we don't know anything about that," he said.
The South has little reverence for the northern government. But the SPLM has so far backed President Bashir in rejecting the ICC warrant.
Southern leaders see good relations with the President's National Congress Party as the best guarantee of the 2005 peace agreement, which calls for national elections this year and a referendum on southern secession in 2011.
But, observers fear that unilateral actions by the northern government, such as the decision to expel the NGOs, may have upset the SPLM, which has already complained that the northern government is not sharing oil revenues evenly and is acting too slowly in implementing the peace agreement.
The southern government continues to avoid public criticism of the northern government on the ICC issue, but Gabriel Changson Chang says the south has done little to conceal it's displeasure with the expulsions.
"Definitely there will be a negative impact, especially on humanitarian services. If they are not there then definitely there will be a gap, a gap that will not be filled by the local NGOs," he said.
The agencies expelled from Darfur have been allowed to continue operating in southern Sudan. But observers fear that areas along the north-south border, whose control is still disputed, could prove problematic.
The so-called "Three Areas", of southern Kordofan, Abyei, and Blue Nile, have long presented the trickiest challenges to north-south peace efforts. Now there is a fear that disputes could arise over the rules for allowing international NGOs to operate.
Hafiz Mohamed, who heads the Sudan program at Justice Africa in London says that these areas, particularly Southern Kordofan, also known as the Nuba Mountains, are particularly dependent on foreign aid.
"In the Nuba Mountains, specifically, it's a big problem. In the area which used to be controlled by SPLM in the Nuba Mountains, 100 percent depend on these organizations especially medical treatment and also education. Because there are no central government services there, they are still relying on these organizations, and most of these organizations have now been expelled," he said.
He says SPLM officials are currently in discussions over how to react.
"I think the SPLM in the Nuba Mountains have to find a way out. They are actually considering different options. And one of the options is to start a system of giving them a license to work in the areas and then they can actually channel their supplies through Lokichogio just like they'd been doing before the signing of the peace agreement," said Mohamed.
The north-south agreement is already extremely fragile. The global financial crisis and the drop in oil prices has had a severe impact on Sudanese finances, particularly in the South. National elections are currently scheduled for this summer, but few think that the country will be ready to carry out a credible exercise by then. And the expulsion of NGOs will add one more challenge.