Renewed Tensions Between Uganda and Rwanda Will Ripple Across East Africa

By Andrew Green Monday, May 7, 2018

Despite a steady stream of denials from Kigali and Kampala, ties between Rwanda and Uganda appear to be deteriorating rapidly. The latest ebb in this historically volatile relationship stems from the Ugandan government’s pushback on what it perceives as Rwandan meddling in its domestic affairs. Though Ugandan officials have not gone public with any formal allegations, their dissatisfaction can be read in a recent string of increasingly high-profile incidents.

Last year, the Ugandan government mounted a crackdown on suspected Rwandan spies operating in Uganda, including the arrest of a handful of Ugandan police officers accused of being part of a so-called sleeper cell carrying out kidnappings and surveillance on behalf of the Rwandan government. And in March, Ugandan President Yoweri Museveni sacked his long-time police chief and security minister, both of whom had close ties to Rwandan President Paul Kagame.

Although the situation doesn’t appear to be heading toward outright conflict in East Africa, this growing animosity could stall attempts to increase cooperation and integration in the region. If it escalates any further, it could also worsen already tense situations in neighboring countries. While war between Rwanda and Uganda is almost unimaginable, proxy battles have sprung from their private disagreements before.

Still, Museveni and Kagame, whose histories are deeply intertwined, have bounced back from worse. Their troubled relationship stretches back decades, to a period before either was in power. During the Ugandan Bush War in the early 1980s, which ended when Museveni seized power from Milton Obote, Kagame served as Museveni’s spy chief. In fact, much of Rwanda’s current leadership cut their teeth in the Bush War with Museveni’s militia, the National Resistance Army.

Members of Rwanda’s Tutsi minority had suffered repeatedly under the majority Hutu population ever since the country won its independence from Belgium in the early 1960s. But the Obote regime proved less than welcoming to Rwandans who fled over the border to Uganda. Museveni provided refuge to the Rwandan exiles in exchange for their support and participation in his rebellion. Many, including Kagame, rose quickly through the NRA’s ranks.

This experience served as a springboard for these Tutsi exiles when they launched their own insurgency against the Hutu government in Rwanda in 1990, under the banner of the Rwandan Patriotic Front. Initially beaten back, they would ultimately seize power in the midst of the 1994 genocide. Kagame was installed first as the defense minister in Rwanda’s post-genocide government later that year, before ascending to the presidency in 2000.

The period after the genocide marked the high water mark of Uganda-Rwanda relations. The two governments collaborated to beat back guerrilla groups menacing their regimes from what was then eastern Zaire, before conspiring to back the rebels who ultimately overthrew Zairian President Mobutu Sese Seko. When the leader they helped install in his place, Laurent-Desire Kabila, forced all Rwandan and Ugandan soldiers out of the newly renamed Democratic Republic of Congo, Kigali quickly backed a new rebel group to overthrow him.

Kampala reluctantly followed suit, but divisions between the two East African governments began to appear. Historians have pointed to personality clashes between military officials and strategic disagreements, but the root of the growing conflict was primarily over resource extraction. Bogged down in an increasingly interminable war, both Rwanda and Uganda were competing to plunder Congo’s wealth.

While war between Rwanda and Uganda is almost unimaginable, proxy battles have sprung from their private disagreements before.
The festering tensions ultimately erupted into a six-day battle in 2000 between Rwandan and Ugandan forces in the town of Kisangani in northeastern Congo. International leaders were involved in quelling the dispute and staving off an escalation, but resentment has lingered.

It took several years and many intermediaries to repair ties between Kagame and Museveni. By 2012, though, Museveni was naming Kagame to the Most Excellent Order of the Pearl of Africa, Uganda’s highest civilian award, in recognition for his role in the Bush War.

Yet that rapprochement did little to curb Kagame’s single-minded focus on protecting his regime—the lesson he learned not just from the genocide, but from decades of Tutsi marginalization. Those instincts seem to have led Rwanda to repeatedly violate Ugandan sovereignty. In 2011, a prominent Rwandan political refugee was assassinated in Kampala. Other regime dissidents have been kidnapped, only to later reappear for trial in Kigali.

Kagame’s administration has consistently denied any involvement and, until recently, Museveni had shown some willingness to overlook these incursions. Now something seems to have changed. Uganda’s political class is awash in rumors that the Rwandan government was trying to orchestrate installing Kale Kayihura, a close Kagame ally in Kampala and the inspector general of police, as Museveni’s eventual successor. Kayihura’s unceremonious firing at the beginning of March has only fanned these rumors.

It could also be that Museveni, still dealing with the fallout from his recent move to lift presidential age limits and pave the way for his eventual re-election to a sixth term, is unwilling to deal with any additional challenges to his authority—and that he is prepared to escalate an issue he was previously willing to handle more privately. Or it might just be saber-rattling from an aging leader looking to assert his continued dominance in Africa’s Great Lakes region.

Kagame’s government has responded mostly with circumspection, though in the wake of last year’s arrests, a number of Ugandans working in prominent Rwandan institutions had their contracts unexpectedly terminated. And both sides continue to insist reports of a rift are overblown. When Kagame traveled to Uganda at the end of March, Museveni took care to emphasize that the two had agreed that their security services should work closely together.

While the current disagreement is unlikely to reach the violence seen in eastern Congo nearly two decades ago, it does have the potential to torpedo regional cooperation. In February, for example, Kagame skipped a health and infrastructure development summit in Kampala. And progress on some elements of a regional trade route that would link the Kenyan port of Mombasa to the rest of East Africa have stalled, though Rwandan officials say that is unrelated to the current political climate.

More worrying is if other hotspots around East Africa become fronts in a renewed cold war between Rwanda and Uganda. The political situation in Burundi is increasingly tenuous, and violence is flaring once again in eastern Congo. Kigali and Kampala already have differing outlooks on how to address both situations. The growing animus between these erstwhile allies could widen those disagreements, with devastating consequences for the region.

Andrew Green is a freelance journalist, based in Berlin. He writes regularly about health and human rights issues. You can view more of his work at