They may be neighbours with strong ethnic and cultural links, but ask any Kampala or Kigali diplomat about the state of their relations and you are unlikely to get a straight answer.

Relations between the two countries have been running hot and cold for the past two decades.

They are currently going through one of the longest stretches of frosty relations and neither side has been willing to admit the seriousness of their disagreement, at least not publicly.

The problem is illustrated in a heap of diplomatic notes — which The EastAfrican has seen — many going without corresponding answers.

Kigali complains that Kampala security agencies, particularly the Chieftaincy of Military Intelligence and the Internal Security Organisation, are conducting a witch-hunt targeting Rwandans living in Uganda.

The documents show various lists of Rwandans they claim authorities in Kampala have detained without allowing them access to relatives or consular officers for help. Kigali also claims that a number of people have been deported to Rwanda without following proper channels.

Court Martial

This accusation is at the heart of the souring relations between the two neighbours as Kampala is currently trying a number of top police officers including former Inspector General of Police Kale Kayihura on charges of aiding or abetting abduction and repatriation of Rwandan refugees in Uganda.

Gen Kayihura was released on bond by the General Court Martial on August 28. Other senior officers remain on trial before the Court Martial.

The most contentious period based on the documents seen by The EastAfrican was between August 2017 and August this year.

Court records of those being tried for kidnap and illegal detention show a more extended period dating back almost five years to 2013.

The index case over this one-year period concerns Rene Rutagungira, who was allegedly kidnapped on August 5, 2017 from Bahama’s Bar in Kampala as recorded in a note verbale dated August 24, 2017. Mr Rutagungira has since appeared in court charged alongside top Ugandan police officers for his alleged role in kidnapping and illegally repatriating Rwandan refugees.

Kigali has also complained of “enemy recruitment in Uganda by the Rwanda National Congress (RNC) with the aim of destabilising the country.”

Rebel outfit

Kigali alleges the RNC is a rebel outfit linked to Kayumba Nyamwasa, a former top Rwanda Patriotic Front official currently exiled in South Africa after he disagreed with his former comrades in Kigali.

Security sources in Kampala claim Kigali has been establishing spy networks mainly through opening of entertainment places like bars and in the transport sector, mainly boda boda taxis, and many of those arrested are employed in or operate such businesses.

The heads of both the Chieftaincy of Military Intelligence and Internal Security Organisation were unavailable for comment and did not return numerous phone calls.

Minister of State for International Relations Okello Oryem and his senior minister Sam Kutesa were not forthcoming with responses to the allegations.

Rwanda’s High Commissioner to Kampala Rtd Maj Frank Mugambage, confirmed Kigali’s accusations of a witch-hunt against its citizens, but remained diplomatic about the state of relations between the two countries.

“I get asked that question many times by the media and others. I believe it is because of certain issues of concern, especially what we see as a kind of witch-hunt against Rwandans. It is believed to be carried out by agents of government, particularly the Chieftaincy of Military Intelligence and the Internal Security Organisation. These cases are of concern because these are Rwandans,” said Maj (rtd) Mugambage.

He admitted to writing to his host ministry several times without receiving any response.

“We have raised these concerns because some of our citizens have been arrested, tortured and others have been sent back to Rwanda leaving their properties behind. We have documented cases but we are yet to receive a sufficient explanation,” said Maj (rtd) Mugambage.

Uganda hosts a significant number of Rwandans, with embassy officials estimating that there could be more than 30,000 Rwandans living in Uganda.

Head of communications at the Rwanda High Commission Kevin Beeza said between 7,000 and 10,000 Rwandans living in Uganda are expected to participate in parliamentary elections starting September 2 at the High Commission in Kampala.