On 29th December, the Rwandan government, through its foreign affairs ministry, wrote a protest note to the Ugandan government condemning what it called ‘multiple unjustified arrests” of its citizens in Uganda without informing its High Commission in Kampala.
This followed the arrest and deportation of five Rwandans living in Uganda through Katuna border post on 28th December.
No reason was given for the deportation executed by the Immigration Directorate.
The latest thorn in the bilateral relationship were the treason charges levied against 45 Rwandans who appeared in a magistrates court Mbarara, southwestern Uganda and were remanded until 15th January.
The strongly worded diplomatic note brought to the fore long-held suspicion that the relations between Kampala and Kigali were souring yet again.
In the protest note, Rwanda claims that Uganda supports rebels allied to Rwandan dissident former Army chief Gen. Kayumba Nyamwasa’s Rwanda National Congress to destabilize Rwanda from the Democratic Republic of Congo (DRC).
But Chief of Defence Forces Gen. David Rubakuba Muhoozi says the allegations are far-fetched.
''We don't harbour any hostile intentions against any of our neighbours and we can’t provide sanctuary to any that may want to destabilise any of our neighbours including Rwanda'' He said
According to the Rwandan government, the discomfort stems from the injustices meted out against their citizens doing legitimate business in Uganda.
From the late 1990s, Rwanda and Uganda have lived through bouts of tension that seem to be resolved, only for the relations to sour again.
So what could be the cause of the new tensions?
Ugandan born Rwandan citizen and former Makerere University senior researcher Dr Frederick Golooba says the rift stems from what Rwanda perceives as bad faith from Uganda on joint regional projects where Uganda seems to be veering away from Rwanda in favour of South Sudan.
''From the Oil pipeline to Power generation, Uganda took a decision without informing Rwanda and Rwanda thinks this is being done in bad faith'' Golooba said.
Uganda reportedly promised to supply electricity to Rwanda through Mirama Hills but this never came to pass.
Rwanda also claims that Uganda's recent alleged forays into Eastern DR Congo in search of the Allied Democratic Front rebels is a guise to arm Rwandan dissident General Kayumba Nyamwasa’s rebel group.
Gen. Nyamwasa fell out with Rwanda's President Paul Kagame and lives in exile in South Africa.
General David Muhoozi who said that the government must address the differences in a more open and candid manner, while Dr Mutebi says he hopes the two countries are big enough to address these behind the scenes.
Uganda’s relationship with Rwanda stretches back to the early 1980s when Ugandan rebel leader, now President Yoweri Museveni and Rwanda's President Paul Kagame took part in Uganda's liberation war.
In 1990, the Rwanda refugees made an attempt to return home by force, led by Major General Fred Rwigyema.
Unfortunately, Rwigyema died in the early days of the fight, forcing Kagame who was away in the united states of America on training to return home and lead his countrymen.
Kagame led the Rwanda patriotic army to victory in Kigali and established the current government that has stabilised Rwanda.