South Sudan: Conflict in Jonglei State Flash Update No. 12 (as of 13 March 2026)

HIGHLIGHTS

  1. The South Sudan Humanitarian Country Team (HCT) and the United Nations Mission in South Sudan (UNMISS) call for peace and civilian protection in Akobo.
  2. Troika envoys urge President Kiir to revoke Akobo evacuation order.
  3. On 6 March, Government forces issued a directive for civilians and aid agencies to vacate Akobo County ahead of planned military operations.
  4. Civilians displaced to Alalai, Akobo East and across the Akobo River to Ethiopia. Additional internal displacement reported from Bor, Jonglei, to Mingkaman, Lakes State.

SITUATION OVERVIEW

Renewed fighting between the South Sudan People’s Defence Forces (SSPDF) and Sudan People’s Liberation Army in Opposition (SPLA-iO) forces since 29 December 2025 worsened the humanitarian situation in several parts of Jonglei State. Akobo, Duk, Nyirol and Uror counties, Jonglei State, are among the most affected areas, with widespread insecurity, destruction of civilian infrastructure and significant constraints on humanitarian access reported. Verified data from the International Organization for Migration (IOM) indicates that more than 267,000 people have been displaced across Jonglei, Lakes, Upper Nile and Central Equatoria States. In Akobo, the security situation remains fluid and unpredictable, following the 72-hour directive by SSPDF on 6 March ordering civilians, United Nations Mission in South Sudan (UNMISS) personnel, UN agencies and non-governmental organizations (NGOs) to vacate the area ahead of a planned military operation. This triggered the mass displacement of an estimated 100,000 people across the border into Ethiopia, in Tergal and Yir‑yir. Other internally displaced people fled to Wanding, Nasir and Ulang, Upper Nile. No humanitarian assistance has reached the displaced populations so far. Communities are surviving on limited food carried during displacement and are sheltering under trees. Immediate needs include food, health services, emergency shelter and non-food items, as well as water, sanitation and hygiene (WASH). Immediate humanitarian assistance is required to address critical needs and prevent further deterioration of the situation.

On 9 March, the HCT in South Sudan issued a statement expressing deep concern over the situation in Akobo County, Jonglei State, following the SSPDF directive on 6 March. Humanitarian partners reported significant cross‑border movements into Ethiopia as well as incidents of looting in Akobo town. The HCT urged all parties to refrain from military operations in populated areas and to resolve differences through dialogue.

Also on 9 March, the UNMISS released a statement calling on all stakeholders to uphold the protection of civilians in Akobo. UNMISS warned that any military operations in and around the area pose serious risks to civilian safety and security and emphasized the need for dialogue. The Mission reaffirmed its commitment to maintaining a protective presence in Akobo and stressed that the safety and security of UN personnel, premises and assets must always be respected.

On 9 March, the embassies of the United Kingdom, the United States of America and Norway (the Troika) urged President Salva Kiir to revoke the evacuation order issued by the SSPDF. According to media reports, the Troika conveyed in a letter that the order could place hundreds of thousands of civilians at risk and further exacerbate the already fragile humanitarian situation in Jonglei State. They reiterated their call for restraint, renewed commitment to peace and adherence to recent peace agreements.

On 7 March, Médecins Sans Frontières (MSF) announced the evacuation of its team from Akobo County in response to the Government evacuation order, leaving thousands without access to primary health care. The evacuation has halted preparations for the malaria season, routine vaccination activities and basic health services for both displaced people and host communities. MSF noted that the order reflects a broader pattern of attacks on health-care facilities. Since March 2025, MSF-supported facilities have experienced 12 security incidents, resulting in three hospital closures. Three additional attacks have already occurred in the first months of 2026. MSF reiterated calls for all parties to protect civilians, safeguard health facilities and ensure secure access to humanitarian assistance. The closure of Akobo Hospital is expected to leave approximately 200 women per month without skilled delivery care, including life‑saving obstetric services for an estimated 30 complicated deliveries.

On 7 March, OCHA, the Deep Field Coordinator and humanitarian partners met with the Akobo County Commissioner, UNMISS (Indian Battalion) leadership, Ethiopian border authorities and local officials in Teirgol, Gambella Region, to discuss contingency planning and response options following ongoing insecurity. While access constraints persist, partners continue to monitor displacement patterns and coordinate with local authorities, UNMISS and Ethiopian officials. Prior to the SSPDF evacuation order, Akobo hosted an estimated 270,000 people, including many displaced people who relied on humanitarian assistance. Women and children represent more than half of the population.

Reports from humanitarian partners indicate that an estimated 100,000 people crossed into Ethiopia since the SSPDF order was issued. Others have moved to neighbouring Upper Nile State, including about 9,000 people in Wanding Payam (Ulang) and approximately 3,500 people in Nasir County. Akobo’s broader population was at an estimated 270,000 prior to the order. Humanitarian organizations have also withdrawn from Akobo, with the first 29 staff relocated to Bor on 8 March. No humanitarian assistance has reached the displaced populations yet. In Bor, Jonglei, about 712 people were displaced across the state’s lines to Mingkaman in Lakes State.

Reports also indicate widespread looting of markets, NGO compounds and Akobo Hospital, the main medical facility serving communities across the county and surrounding areas. A total of 25 medical staff and vulnerable patients were relocated to Juba with the rest of the patients self-relocating elsewhere due to the heightened tensions. The hospital now stands empty. Ninety-nine wells in the town have reportedly been destroyed or contaminated.

HUMANITARIAN IMPACT AND NEEDS

  1. Cholera Outbreak: Between 4 March and 10 March, health partners reported a total of 101 new cholera cases and six deaths, representing a case fatality rate of 5.9 per cent. The new cases were recorded in Ayod (42), Duk (28), Yirol East (17), Bor South (6), Uror (5), Awerial (2) and Juba (1), with Bor South and Awerial marking a resurgence of infections. All six deaths resulted from severe dehydration and occurred in Ayod (5) and Uror (1). This brings the cumulative total to 100,646 cholera cases and 1,652 deaths across 55 counties in nine states and all three administrative areas since the outbreak began on 28 September 2024, indicating continued spread of the disease.
  2. Health facilities functionality: The health situation has deteriorated significantly in Akobo County. Of the 15 health facilities, seven are non-functional due to conflict-related damage, including Walgak PHCC, which was reportedly hit by an airstrike, and Tangnyang PHCC, which was vandalized during recent fighting. A key concern is waning disease immunity as vaccination campaigns are stalled or interrupted due to ongoing conflict while the threat of outbreaks of measles, cholera, meningitis and severe acute malnutrition persists.
  3. Widespread looting has been reported, including, NGO compounds and Akobo Hospital. NGO assets, including vehicles stored at the UNMISS temporary operating base, remain secure. UNFPA reported that approximately 25,000 dignity kits, along with unspecified protective health kits, were looted. OCHA and partners have initiated documentation of all looted items.
  4. Looming water crisis in Akobo: The looting and destruction of solar panels at Akobo's main water-pumping station has left the facility non-functional, severely disrupting access to safe water at a time of mass displacement and heightened vulnerability. The loss of this critical infrastructure compounds the humanitarian situation across Akobo County, where public facilities, including water systems, have been repeatedly targeted amid weeks of intensified conflict. Restoring the facility could take time and resources, raising concerns about access to clean water in an area with limited alternative water infrastructure.
  5. Humanitarian access: In February 2026, 72 humanitarian access incidents were reported, bringing the total to 134 incidents for January-February. Violence against humanitarian personnel and assets accounted for the largest share, with 52 incidents, while six incidents of active hostilities directly affected humanitarian operations. Four humanitarian workers were killed in Jonglei State. Seven staff were evacuated from Ulang County, Upper Nile, amid escalating clashes in Jonglei State, Upper Nile State and Unity State. The ongoing clashes between SSPDF and opposition forces in Akobo and Canal/Pigi (Jonglei) and Ulang and Nasir (Upper Nile) forced the relocation of at least 45 humanitarian staff between 5 and 8 March.
  6. IDP verification and registration: On 6 March, humanitarian partners conducted registration and verification of internally displaced persons (IDPs) across Akobo to ensure assistance reaches newly displaced and highly vulnerable communities. IOM led the registration in Bilkey Payam and surrounding bomas, targeting households recently affected by displacement; approximately 1,800 households would receive emergency shelter and non‑food items (NFIs). Community Initiative for Development Organization (CIDO) registered about 1,500 households in Dengjok and Nyandit payams which will receive materials for temporary shelter construction and reinforcement. Save the Children International (SCI) identified 481 previously unregistered households for assistance, who will receive cash support after registration.
  7. World Food Programme (WFP) pauses registration for assistance: On 4 March, WFP temporarily paused IDP registration in Akobo County, citing acute food shortages among the displaced communities. Before the pause, the verification team had registered 2,000 households (approximately 12,000 people) previously displaced from Walgak and Nyirol counties. An appropriate mode of assistance will be determined before moving forward.

HUMANITARIAN RESPONSE AND CHALLENGES

  1. Logistics Cluster Dispatched First Convoy with Aid Supplies: On 11 March, the Logistics Cluster successfully dispatched its first convoy from Bor to Ayod and Nyirol counties. The convoy comprised seven trucks and one light vehicle, transporting 160 metric tonnes of water, sanitation and hygiene (WASH) and nutrition supplies bound for Ayod, Mogok, Yuai, Pieri and Pathai. The mission encountered no bureaucratic impediments, following a successful WFP‑led access mission to the same locations the previous day. Local authorities in Ayod provided assurances regarding the safety and security of humanitarian personnel and aid recipients. Humanitarian teams also reported that civilians in Pagak and Magok payams had relocated to swampy areas for safety, while in Palouny and Pathai payams, widespread infrastructure damage was observed alongside efforts by affected communities to rebuild.
  2. Coordination with Ethiopia: OCHA South Sudan engaged with OCHA Ethiopia to share updates on the situation and support preparedness for a potential influx into Ethiopia. On 9 March, a Cluster Lead Agency (CLA) meeting in Addis Ababa discussed scenarios related to cross‑border population movements. Partners in Ethiopia highlighted concerns regarding limited government responsiveness and lack of clarity on refugee reception and registration arrangements. Partners reported that an estimated 100,000 people have relocated to Ethiopia.
  3. On 13 March, the Humanitarian Coordinators (HCs) for South Sudan and Ethiopia convened a meeting to share information and to strengthen coordination as a result of the latest impacts and situation in Akobo.

CHALLENGES

  1. Access constraints persist in multiple locations: Akobo County remains completely inaccessible to humanitarians following the 6 March SSPDF order. In addition, humanitarian access to Lankien, Waat, Walgak, Boung, Wecjal and Kaikuiny remains restricted due to sporadic clashes, limiting the ability of partners to deliver assistance and conduct assessments.
  2. Population movements complicate beneficiary verification: Ongoing displacement from Akobo and other parts of Jonglei State and surrounding areas, coupled with limited communication networks, continues to hinder partners’ ability to verify beneficiary figures and update population data.

FUNDING

US Government allocates US$100 million through SSHF to scale up life‑saving assistance: The United States Government has allocated US$100 million through the South Sudan Humanitarian Fund (SSHF) Reserve Allocation to support rapid, life‑saving assistance for 1.3 million people facing the most severe humanitarian needs (severity levels 4 and 5 under the 2026 Humanitarian Needs and Response Plan). The allocation targets internally displaced people, refugees and vulnerable host communities across 18 priority counties in Upper Nile, Unity, Jonglei, Warrap, Northern Bahr el Ghazal, Eastern Equatoria and the Abyei Administrative Area. Funding will address severe acute malnutrition, critical protection risks and significant gaps in essential basic services. The allocation was launched on 4 March 2026 and project proposal review is ongoing.