Soldiers from the South Sudanese army (SPLA) assembled in the capital, Juba on 8 January 2014 (Photo: Mehmet Kemal Firik/Anadolu Agency/Getty)

Senior government’s officials including the Presidential Advisor on Security Affairs and the Minister of Defence described the statement by the United States as “unfortunate”, saying it could undermine current efforts to resolve security matters in the young country.

“This is unfortunate and we will ask clarification from relevant institutions through diplomatic channels. It undermines the current efforts to handle such matters. There are already mechanisms through which such allegations could be addressed and the United States is one of the players we expect to play a positive role,” Presidential Advisor on Security Affairs, Tut Kew Gatluak, told Sudan Tribune on Friday.

While the Presidential Advisor on Security Affairs, Gatluak, did not deny or confirm the existence of the Sudanese rebels inside South Sudan and whether the government provides any support them, the Defence Minister, Kuol Manyang Juuk, admitted the Sudanese rebels were being harboured in the country in the past, but added that the government had already ordered them to leave the country or handover their guns and go to refugee camps set up in the country.

“It is not true. There are no Sudanese rebels in the republic of South Sudan. We have ordered them to leave South Sudan and go back to Sudan or hand over their weapons and go to refugee camps,” minister Juuk said in a separate interview with the Sudan Tribune.

“If they agree to go to the refugee camps, we will collect the guns and call Sudan to inspect them and hand them over because we would not need” the firearms,” he added.

His statement implies that the country was still hosting Sudanese rebels and was now in talks with them to either leave the country or go into refugee camps. Such assistance, according to the statement of the United States, places South Sudan in violation of a United Nations Security Council resolution as well as numerous agreements between Juba and Khartoum.

Aid to Sudanese rebels also violates the internal peace agreement signed last year by President Salva Kiir. The U.S. statement indicates that Sudanese armed groups remain involved in conflicts inside South Sudan.

“The presence of Sudanese armed opposition forces in South Sudan, and their involvement in South Sudan’s internal conflicts, destabilises both Sudan and South Sudan,” the U.S. State Department spokesperson said in a statement Sudan Tribune obtained on Thursday.

“We call on the government of the Republic of South Sudan to ensure Sudanese armed opposition groups are not in a position to conduct armed operations within South Sudan or across the border in Sudan,” the statement added.

The Thursday’s statement highlights the Obama administration’s growing estrangement from President Kiir’s government as well as signs of reconciliation between Washington and Khartoum.

The State Department said last month that the U.S. “welcomes Sudan’s recent efforts to increase counterterrorism cooperation with the United States.”

The U.S. said at the time that Sudan’s government has sought to prevent the movement of Islamic State members into and through its territory. “Subject to and consistent with? US law, we will work cooperatively with the government of Sudan on counterterrorism to enhance the security of both our countries,” the State Department announced on 20 September.

Observers in South Sudan are keen to emphasize that the statement by US is a move designed to put pressure on the government of South Sudan to accept deployment of regional protection force and implement the 2015 peace agreement it signed with the armed opposition leader, Riek Machar.

The government of South Sudan has been always accused by the Sudan, various observer groups and armed oppositions of harbouring Sudanese rebels and in fact letting them fight alongside its own force. The government in Juba has always denied the accusations.