Officials confirm at least six fatalities, with casualties reported on both sides, and several civilians seriously injured.

According to statements from the South Sudan People’s Defense Forces (SSPDF), a Ugandan contingent allegedly attacked a border outpost near Pogee in Magwi County, resulting in two fatalities among South Sudanese soldiers and additional injuries.

Meanwhile, the Uganda People’s Defence Forces (UPDF) assert that their troops responded after South Sudanese soldiers advanced into what they maintain is Ugandan territory—denying wrongful aggression but acknowledging cross-border shots.

Adding to the toll, local authorities in the border town of Moyo, Uganda, reported retaliatory incidents: South Sudanese youths crossed into Uganda, killing five Ugandans, and prompting subsequent responses by Ugandan youths inside South Sudan. These tit‑for‑tat attacks involved arson, rape allegations, and cattle theft across the border.

The death toll—originally reported as two from each side—was later revised, with defenseWeb/defenceWeb and other sources putting the confirmed fatalities at seven, including both civilians and soldiers. Officials from South Sudan said two of their soldiers died, while Uganda reportedly suffered five casualties among civilians and security personnel.

Border Disputes History: Tensions between South Sudan and Uganda have persisted for years, rooted in contested border demarcations in Magwi and Kajo Keji counties, with prior deadly incidents dating back to 2020 and 2024.

Ugandan Military Presence: In early March 2025, Uganda deployed special forces to help secure South Sudan amid internal unrest involving President Salva Kiir and Vice President Riek Machar. That deployment heightened the potential for friction along poorly defined frontiers.

Humanitarian & Security Fallout

Thousands have reportedly been displaced. Residents are sheltering in schools, churches, and bush camps across both sides of the border, as authorities struggle to contain violence and mitigate refugee flows.

South Sudanese and Ugandan leaders have initiated diplomatic engagement. On-site commanders have been instructed to avoid further escalation, and investigations are underway to determine the origins and responsibility for the skirmishes.

Regional stability risk: These clashes threaten to inflame a broader security crisis in a region already fragile from internal conflict, refugee crises, and economic strain.

Weak borders: Lack of clear demarcation and competing claims fuel recurring eruptions of violence between state security forces and local communities.

Mixed civilian‑military toll: The incidents blur lines between battlefield and population centers, with civilians bearing much of the hardship across the border.

A joint border demarcation committee (established in 2017) is under pressure to reconvene and deliver tangible progress to prevent future flare-ups.

Both capitals – Juba and Kampala—face calls to press for de-escalation, strengthen cross-border communication, and ensure compensation and security for affected civilians.

These deadly skirmishes underscore how unresolved border disputes, even between allied neighbors, can spiral into bloodshed, especially when civilian communities—often unrepresented—bear the brunt.

Let me know if you’d like follow-up profiles on affected regions, displaced communities, or peace negotiations evolving around this incident.

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The videos, which sparked violent protests and retaliatory killings across South Sudan, have since been removed, according to a Jan. 27 statement from the National Communications Authority directed at telecom and internet providers.

The country’s telecommunication authority blamed the rise of violence to the social media.

“The rise of violence linked to social media content in South Sudan underscores the need for a balanced approach that addresses the root causes of online incitement while protecting the rights of the population,” said Napoleon Adok Gai, director of the National Communications Authority.

Rights groups have accused the Sudanese army and its allies of carrying out ethnically targeted attacks on civilians in Sudan’s El Gezira state earlier this month, following their capture of Wad Madani, the state capital, from the paramilitary Rapid Support Forces.

In response, the Sudanese army condemned the incidents as “individual violations” captured on video and widely shared on social media.

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The organizations published a joint letter to parliament detailing the bill’s problematic provisions as well as several positive provisions.

“An in-depth review and revision of outstanding gaps in the law governing the National Security Service is critical to reining in the notorious agency,” said Mausi Segun, Africa director at Human Rights Watch. “Parliament needs to ensure that the pending law genuinely limits the security service’s powers and strengthens oversight of the agency’s activities.”

The current National Security Service Act of 2014 gives the agency broad and unqualified powers that allow it to commit serious abuses with impunity, creating and sustaining a climate of repression and fear.

Human Rights Watch and Amnesty International among other rights organizations have documented that the security agency’s broad powers have contributed to shrinking civic space. The agency exerts its authority without meaningful judicial or legislative oversight, agents are rarely punished for abuses, and the government lacks the political will to address these widespread practices, the organizations said. These abuses have left many victims with long-term physical and mental health conditions.

The bill to amend the 2014 law currently before parliament was drafted by the National Constitutional Amendment Committee (NCAC) as part of the reforms initiated by the Revitalized Peace Agreement of 2018. Following lack of consensus by committee members about the agency’s authority to make arrests, the bill was referred to the Justice Ministry in 2019 and then to the presidency in April 2021 for resolution.

In December 2022, the justice minister recommended to the cabinet and presidency that the agency’s authority to arrest and detain suspects should be limited. On February 22, 2023, several media outlets reported that the presidency had agreed to abolish the agency’s authority to arrest and detain people, with or without a warrant. On May 9, media reported that the bill would be presented for its first reading in parliament within two weeks, which has since elapsed.

The bill includes a series of positive provisions, Amnesty International and Human Rights Watch said. It introduces guiding principles founded on a respect for human rights and prohibits torture, cruel, inhuman and degrading treatment; and prohibits detention or confinement by security agents. It also gives the justice minister and civilian courts a greater role in prosecuting agency officials accused of crimes. However, the bill still contains vague and broad provisions that would allow the agency to continue to abuse human rights, the organizations said.

While the Bill revokes sections 54 and 55 of the National Security Service Act, which gave the agency the authority to arrest with or without a warrant, it retains its arrest authority “under emergency circumstances,” which could be subject to abuse. It also allows arrests without a warrant in section 57, if the person is suspected of broad “crimes against the state.”
During the bill’s review, parliament should remove this power of arrest, the organizations said.

Further, while section 57 gives any magistrate powers to visit any detention site, this section read together with section 13(15), which would allow the agency to arrest people under certain circumstances suggests that the agency can hold people in custody. Parliament should make clear that the agency cannot detain civilians under any circumstances, Human Rights Watch and Amnesty International said.

The bill’s overly broad definition of “crimes against the state” as “any activity directed at undermining … the government” and reference to the same crime in the 2008 Penal Code Act, which is equally vague, is problematic. The government has in the past used trumped-up charges of crimes against the state to restrict the rights to freedom of expression, peaceful assembly, and association, including peaceful exercise of political opposition, or public criticism of state policy and actions.

In the meantime, the South Sudanese government should order the closure of all unauthorized detention sites operated by the security agency and release detainees or hand them over to legitimate law enforcement officials for charge and fair trial. The authorities should also disclose the whereabouts, status, and condition of Morris Mabior Awikjiok, a South Sudanese refugee transferred from Kenya in early March. He is reportedly being held incommunicado at the security agency’s Blue House detention site.

“For the efforts to reform the security service to be impactful, they must be accompanied by measures to hold officers to account for past and ongoing rights abuses,” said Tigere Chagutah, Regional Director at Amnesty International’s East and Southern Africa Regional Office. “Authorities should ensure that security service officials, including senior officials, are held to account.”

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This decision has been welcomed by Amnesty International’s Regional Director for East and Southern Africa, Tigere Chagutah, who sees it as a crucial step towards protecting the millions of civilians who have endured a decade-long conflict marked by atrocities such as rape and other forms of sexual violence.

Chagutah emphasized the importance of the arms embargo in preventing the flow of weapons into South Sudan, which have been consistently used to commit heinous crimes with impunity.

The extension of the embargo sends a clear message to the South Sudanese government that urgent action is required to implement the Joint Action Plan on addressing conflict-related sexual violence, as well as other benchmarks set by the Security Council under Resolution 2577 of May 2021.

While Amnesty International views the extension of the arms embargo as a positive step, there is concern regarding the provision that allows South Sudan to import “non-lethal” equipment without informing or seeking an exception from the Security Council’s sanctions committee. Research has shown that security forces in the country have misused less lethal weapons to violently suppress peaceful protests, causing severe injuries and deaths.

Amnesty International further calls upon the Security Council to ensure the implementation of effective measures to control the flow of weapons into South Sudan. Violators of the arms embargo, whether they are states, businesses, or individuals, must be held accountable for their actions.

The UN Commission on Human Rights in South Sudan, the UN Panel of Experts, and the Secretary General’s recent reports to the Security Council have all highlighted the increasing cases of conflict-related sexual violence and the lack of progress in implementing the Joint Action Plan.

In a 2022 report, Amnesty International emphasized how government soldiers, opposition-aligned groups, and non-state armed groups in South Sudan use firearms to perpetrate conflict-related sexual violence.

The Security Council initially imposed the arms embargo on South Sudan through Resolution 2428 in 2018 and has since renewed it multiple times, with the most recent renewal occurring via Resolution 2633 in 2022. Resolution 2577, adopted in 2021, expressed the Security Council’s willingness to review the arms embargo measures based on an assessment by the Secretary-General of progress made towards five benchmarks.

These benchmarks include the completion of the Strategic Defence and Security Review process outlined in the Revitalised Agreement on the Resolution of the Conflict in the Republic of South Sudan (R-ARCSS), the establishment of the Necessary Unified Forces, progress in the disarmament, demobilization, and reintegration process, proper management of existing arms and ammunition stockpiles, and implementation of the Joint Action Plan for the Armed Forces to address conflict-related sexual violence.

According to the UN, the implementation of these benchmarks has been minimal or non-existent, indicating a lack of progress in South Sudan’s commitment to peace and the protection of human rights.

The extension of the arms embargo serves as a reminder to the South Sudanese government and the international community of the pressing need for meaningful action to end the suffering of the country’s civilians and bring about lasting peace and stability.

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“The decision of the Council to renew the CHRSS is an important signal from the Human Rights Council that accountability is key, as South Sudan embarks on the extended phase of the 2018 revitalized peace agreement. The pervasive impunity in South Sudan perpetuates cycles of violence. In this context, the CHRSS plays an invaluable role in collecting and preserving evidence of crimes under international law, which can be used for future prosecutions.

“In South Sudan, people are still living amid armed conflict and regularly face attacks, unlawful killings, displacement and rape. Many people also suffer from limited access to water, food and basic medical health care, in part due to the high levels of insecurity. The human rights concerns that necessitated the creation of the CHRSS in 2016 continue to persist, and the government has done too little to warrant the lifting of scrutiny by the Council. We deeply regret the efforts of some states, including the Government of South Sudan, to block the renewal of this vital mechanism.

“South Sudan must urgently improve its human rights situation by holding perpetrators of war crimes and other violations of humanitarian law to account. The country should also cooperate fully with the CHRSS as it continues its important work.”

Background

In March 2016, the UN Human Rights Council established the CHRSS and mandated it to “collect and preserve evidence of, and clarify responsibility for alleged gross violations and abuses of human rights and related crimes, including sexual and gender-based violence and ethnic violence, with a view to ending impunity and providing accountability, and to make such information available also to all transitional justice mechanisms.”[1] In addition, the Commission also has an important task of providing technical assistance to the Government of South Sudan to establish a holistic transitional justice programme enshrined in the 2015 and 2018 peace agreements.

Since 2016, the resolution renewing the Commission had been adopted by consensus, yet in March 2021, South Sudan rejected a renewal of the mechanism.

This year, the resolution was adopted by a vote of 19 in favour, 09 against, and 19 abstentions.

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