The strained relationship between Uganda and Sudan deteriorated further last week, with Khartoum recalling its ambassador to Kampala Hussein Awad Ali, over long held suspicions that Uganda was harbouring Sudanese rebels.

Sudan accuses Uganda of supporting and sheltering rebels fighting against the regime in Khartoum, while Uganda has in the past accused President Omar al Bashir’s government of fighting a proxy war against it by sponsoring the Lord’s Resistance Army (LRA) rebels.

Diplomatic sources said the Sudan ambassador to Uganda left the country on Thursday. Uganda confirmed that the ambassador left upon being recalled by his government.

However, some diplomatic sources said the diplomat was asked to leave after intelligence reports linked him to espionage. The same sources added that Uganda was expected to recall its ambassador in Khartoum.

“They have recalled the ambassador and it is their prerogative. Because we had already explained our position to them — that while they (Sudanese rebels) are here, they are not allowed to engage in subversive activities,” said Foreign Affairs spokesperson Fred Opolot.

“What Uganda has done is to give shelter to their families; and of course they come in to visit their families but are not allowed to launch any war from here.”

Uganda expelled a Sudanese diplomat late last year over alleged espionage. Kampala accused Jad-el-Seed Mohammed Elhag of involvement in “activities beyond the norm.”

READ: Uganda uncovers Sudanese spy ring, reviews security

In January 2013, Sudan lodged a complaint against Uganda with the African Union and the International Conference on the Great Lakes Region, after the opposition political parties and Sudan rebels signed an agreement dubbed “New Dawn” in Kampala whose aim, Khartoum said, was to overthrow the regime.

But Uganda has denied having any intentions of overthrowing the Khartoum regime or supporting any rebel group with the intention of regime change.

The latest breakdown of relations comes after a few years of détente that saw South Sudan break away from the North in 2005 and a final routing of the LRA to the jungles of Central Africa.

It was not immediately clear how or whether the renewed tensions between Sudan and Uganda are in any way connected to the ongoing conflict in South Sudan, where Kampala is backing President Salva Kiir’s government, which this week lost a key oil town — Bentiu — to former vice-president Riek Machar’s forces.

South Sudan, however, is accusing the North of arming rebels in support of Machar.

Though Sudan denies supporting any rebel group in the South and President al Bashir has visited and declared his support for the Salva Kiir government, SPLA government officials and military commanders say rebels loyal to Machar are being trained on Sudan soil near the oil-rich states.

For Khartoum though, the decision to recall Mr Awad Ali could see a total collapse of efforts to patch up relations between Uganda and Sudan that were started by the Jimmy Carter Centre in the mid 2000s.

Also, the recall means the end to an effort by a committee that was put in place by foreign affairs ministries of the two countries to try and calm the emerging diplomatic war.

Though Uganda’s President Yoweri Museveni and Sudan’s President al Bashir met last year on the sidelines of the AU summit in Addis Ababa to discuss contentious issues and ways of improving the strained relationship, sources said they failed to reach a conclusive agreement.

“President Museveni told Bashir in that meeting that while he was a rebel, Sweden gave his family a safe place to stay and what he is doing is give the families of the rebels a safe place to stay but not support the rebel activities,” said a source privy to details of the meeting between the two leaders.

President al Bashir, however, insisted that Uganda expel the rebel leaders.

Kampala and Khartoum have over the years traded accusations over support for each other’s rebel groups.

President al Bashir supported the LRA rebel group, which terrorised Northern Uganda for two decades while President Museveni was a personal friend of the late John Garang and supported the Sudan People’s Liberation Army (SPLA) in its fight for the South’s independence.

In May 2012, President Museveni said that his government had received intelligence that the LRA were rearming and warned Khartoum, saying the LRA were receiving weapons from Sudan.

Kampala, in a bid to put pressure on Khartoum, opened its door to Sudanese rebel leaders two years ago.

Several meetings held before and after the two heads of states met to defuse tension between the two countries to settle the issues have failed as Kampala insists that Sudan should help in arresting LRA leader Joseph Kony, whereas Khartoum maintains that it has no contacts with the elusive rebel leader.