Uganda denies air force targeted civilians in South Sudan conflict

Uganda has rejected a United Nations report accusing its air force of bombing South Sudanese communities, describing the findings as “not exhaustive” and criticising media coverage of the military operations as biased and failing to reflect Kampala’s position.

On February 27, the UN Commission on Human Rights published a report detailing the alleged use of improvised incendiary devices by the air force.

The report also said the Uganda People’s Defence Forces (UPDF) had deployed infantry units to support South Sudanese forces in ground operations, specifically targeting the Nuer community.

The bombings were reported after the UPDF launched Operation Mlinzi wa Kimya, deploying air force commandos and ground forces in Juba in March 2025 at the request of South Sudan President Salva Kiir. The deployment formed part of Uganda’s wider military intervention to stabilise the government in Juba.

Fragile peace

The deployment followed escalating tensions between President Kiir and First Vice-President Riek Machar after a militia allied to the VP attacked a military garrison near the Ethiopian border, threatening the fragile power-sharing arrangement between the two rivals.

“The current UPDF operation in South Sudan is completely legitimate,” army spokesperson Col Chris Magezi said in a statement issued on Tuesday.

“UPDF was invited by the sovereign government of the country, and the deployment was approved by the Parliament of Uganda. UPDF has never targeted civilians in its 45-year cherished history, which is why it is extremely popular with the people wherever it operates.”

However, South Sudanese opposition politicians have accused the Ugandan air force of supporting the South Sudan People’s Defence Forces (SSPDF) in bombing civilians in the volatile Upper Nile state, where the Machar-allied White Army militia had threatened to advance towards the capital, Juba.

The allegations have previously fuelled controversy over Uganda’s military role in the country.

Civilian toll

In June, South Sudanese politician Dei Tut Weang Khor resigned his seat in the Transitional National Legislative Assembly over the war in Upper Nile state. Khor represented Nasir County, the epicentre of the conflict, where bombs had reportedly been falling on civilians for months.

He also resigned from the Pan-African Parliament, citing a moral dilemma in serving a government he said was bombing its own citizens, as airstrikes by the Ugandan air force-backed SSPDF intensified in Nasir.

Aid missions

Local media reports later indicated that the Ugandan air force shifted its focus to humanitarian operations, including emergency food airdrops in conflict-affected areas of Upper Nile state, where thousands of displaced people faced starvation.

Critics, however, viewed the shift as an attempt by the government and Ugandan forces to deflect attention from criticism over alleged airstrikes on civilians.

But Col Magezi told The EastAfrican that Uganda’s involvement in the food deliveries came at the request of the South Sudan government.

“We are much obliged to support our brothers whenever they need us. Humanitarian aid operations will continue for as long as necessary. Until the humanitarian situation improves,” he said.

Arms embargo

The UN report said aerial bombardments and ground operations following the Ugandan deployment caused widespread devastation, including civilian deaths, injuries, and destruction of homes. It also suggested that Kampala may have violated the United Nations arms embargo imposed on South Sudan.

“UPDF has, over the years, conducted successful military and peace support operations in Somalia, in Eastern DRC, and in South Sudan. The people of South Sudan are happy with UPDF operations in the country, which prevented internecine fighting in Juba and stopped the White Army’s atrocities against the population,” Col Magezi said.

He added that Uganda’s involvement in South Sudan is based on continued political dialogue between the government and opposition parties, implementation of the power-sharing agreement, prevention of widespread violence, and maintaining regional stability.