In a move that could be indicative of shifting alliances, Kampala is ditching its decades-long backing for dissidents opposed to Sudan’s President Hassan Omar al-Bashir in exchange for a normalised relationship with Khartoum.

Following horse-trading between President Museveni and a delegation from the North African country on February 8, both sides announced that Uganda had undertaken to expel leaders of the Justice and Equality Movement and other anti-Khartoum revolutionary forces that had found sanctuary in Kampala.

Ministry of Foreign Affairs spokesperson Fred Opolot said that, at the meeting with President Museveni, the delegation led by Sudan Vice-President Hasabo Mohamed Abdalla raised its concerns about Uganda’s continued hosting of anti-Bashir outfits.

In response, their host said he did not support hostile activities by such groups and then instructed security agencies to investigate the concerns. The culprits would be repatriated to Sudan — in much the same fashion some active anti-Khartoum rebels were kicked out last year.

The Sudanese delegation, in Kampala at the invitation of President Museveni, comprised the head of the national intelligence and security service, the interior minister and Junior Foreign Affairs Minister Obeid-Allah Mohamed.

The development came amid reports — denied by Kampala — of a recent altercation in Addis Ababa in which the leaders of the two countries accused each other of stalling the South Sudan peace process, as well as claims of a subsequent build-up of Sudanese forces on its border with South Sudan.

READ: Regional interests shaping South Sudan war

The Uganda People’s Defence Forces have been propping up South Sudan President Salva Kiir’s government against an onslaught by rebels allied to his former vice-president-turned-foe Dr Riek Machar since December 2013.

“It is true we are trading the leaders of Sudanese rebel groups based here in return for normalisation of the relationship that has been hostile for more than 25 years,” Minister of State for International Affairs Henry Okello Oryem told The EastAfrican.

Khartoum has not had a full ambassador posted to its mission in Kampala since the severing of bilateral ties in 1995, at the height of a proxy war in which Sudan backed the Lord’s Resistance Army rebels in retaliation for Kampala’s support of the Sudanese People’s Liberation Movement, which went on to secede and found the Republic of South Sudan in 2011.

Intelligence sources said Kampala would later raise the heat on Khartoum by helping Sudanese opposition groups to open new fronts in western and northern Sudan.

Although diplomatic relations were restored in 2005 on the shoulder of the South Sudan peace process, the situation is tantamount to having no diplomatic relations at all, according to Mr Oryem. 

In October 2013, Uganda expelled Jad-el-Seed Mohammed Elhag, a Sudanese diplomat accused of attempting to buy classified documents from state employees.

READ: Uganda uncovers Sudanese spy ring, reviews security

This week’s meetings however resolved to restore full diplomatic relations and establish a Joint Permanent Commission to manage other aspects of co-operation in areas such as trade and security.

An ebullient Obeid-Allah Mohamed said in Khartoum on February 10 that security had dominated the talks, with President Museveni pledging to expel anti-Sudan rebels. He corroborated Mr Oryem’s assertions, saying “a follow-up mechanism was established to monitor the meeting’s outcome, especially in terms of security.”

Major conflagration

Independent sources reported that Sudan had raised its troop presence on the border with South Sudan. They predicted a major conflagration that would suck in Uganda in a matter of weeks.

Without clarifying Uganda’s sacrifice of its long-term alliance with Sudanese rebels, Mr Oryem said it was not a knee-jerk response to emerging threats as suggested by regional security analysts, who say Khartoum had received significant funding from a Persian Gulf state to support a military campaign in South Sudan. He also dismissed as untrue reports of an altercation between Presidents Museveni and al-Bashir in Ethiopia.

President Museveni returned to Kampala from the last Igad meeting on the South Sudan conflict in Addis then almost immediately headed to Juba to meet President Kiir. Last week, Uganda announced that Juba had extended the pact under which Ugandan troops are operating in South Sudan.

“There have been sustained efforts on numerous fronts to reconcile Uganda and Sudan and this is the outcome,” Mr Oryem told The EastAfrican, adding: “Reports of a troop build-up by Uganda in Juba are nonsense because we have the force multipliers to defend our troops in Bor, which is the farthest point where we have a troop presence in South Sudan.”

Mr Oryem, who managed President Museveni’s schedule at the recent AU meetings in Addis, also said there was no meeting planned between the two presidents.

“[Zimbabwe’s President Robert] Mugabe was the only person His Excellency was supposed to meet but the plans fell through after he was elected AU chair and he could not leave the podium to meet President Museveni, who had to leave early because he had only one day in Addis Ababa,” he said.

President Museveni however held talks with Presidents Abdel Fattah el-Sisi of Egypt and Kiir as well as a delegation from Abu Dhabi.

While Uganda downplays the emerging tensions, James Morgan, the charge d’affaires of the South Sudan mission in Nairobi, said he would not be surprised if Sudan were mobilising forces against South Sudan because Khartoum had never been happy that Juba seceded. He said Sudan had been supporting the Machar group because most of the rebel commanders, such as Peter Kadet, are based in Khartoum.

Additional reporting by Barbara Among and Fred Oluoch,