South Sudan's Military Accused of Systematic Destruction in Jonglei Counteroffensive

In early February, as South Sudan's military pushed eastward through Jonglei State, the hospital in Lankien stood empty. Doctors had spent the previous days evacuating patients—some in active labour, others with gunshot wounds—racing against time as fighting intensified around the town. On the evening of February 3, hours after the last patient was carried out, a bomb struck the facility, tearing through its warehouse and leaving a crater in the rubble. By the time residents were forced to flee into surrounding marshland four days later, the hospital had been reduced to ash and twisted metal. Its vaccine storage unit was burned. Vehicles were stripped for parts. The market was obliterated. Homes on the town's edge were charred black.

This was not an isolated incident. Across a swath of Jonglei State stretching from the Nile River toward the Ethiopian border, a pattern of destruction unfolded between late January and February. The Centre for Information Resilience, using satellite imagery combined with verified video and witness testimony, documented more than two dozen incidents of systematic burning and looting. In nearly all cases, civilian structures—hospitals, markets, homes—bore the marks of deliberate destruction. Troop movements tracked by satellite appeared to follow a path of burning as forces advanced from west to east, according to researchers who analyzed the data. The destruction was "likely to be more widespread and potentially part of what it described as a deliberate military strategy," the organization concluded, though satellite imagery alone cannot determine intent or assign responsibility.

The military campaign, announced on January 28 and called "Operation Enduring Peace," was launched after opposition fighters seized several military garrisons in December and January. The government mobilized forces drawn from the national army, intelligence units, police, and allied militias to retake the territory. The involvement of these allied groups has made it difficult to establish clear lines of command responsibility. Government officials did not respond to requests for comment on the specific allegations, though authorities have previously stated that military operations are conducted in self-defense and that civilians are not deliberately targeted. Opposition representatives deny that their forces were present during the attacks on civilian areas, though these accounts could not be independently verified due to restricted access to the region.

The human toll emerged through the accounts of those who lived through the attacks. Gai Ket, 32, was cutting firewood when explosions began in Lankien on February 7. He rushed back to find his house engulfed in smoke. His wife lay dead inside, a severe wound to her chest. Bodies were scattered across the neighborhood. "Everything was gone," he said. Another resident, Puoch Duol, returned at night searching for his grandmother, who had been too weak to flee. He found her body among several others near the ruins of burned homes. Five individuals who fled Lankien described the same sequence: government-aligned forces arriving in armoured vehicles after opposition fighters had withdrawn, followed by mortar fire, then ground troops moving through the town setting fires and killing civilians.

The destruction extended far beyond Lankien. In Walgak, an aid worker named Jany witnessed the same pattern on February 5: smoke everywhere, gunfire, houses burning. Satellite imagery confirmed significant structural damage in the town between February 3 and 7. Multiple villages in the vicinity were burned or destroyed during the same period, according to humanitarian sources tracking developments, though ongoing insecurity prevented independent verification. In Pathai, geolocated social media footage showed fighters moving among burning structures, though the identities of those in the footage could not be independently verified.

Concerns about civilian safety had surfaced even before the operations began. A video circulated on social media showed Johnson Olony, a deputy army chief and head of an allied militia, telling troops not to spare lives or property during operations. The government later said the remarks did not reflect official policy, and Olony apologized. In another video, a commander identified as Wal Nyak appeared to threaten violence against perceived opposition supporters, saying "Whether you are a woman or a girl, we will kill you all." The authenticity and full context of these videos could not be independently verified.

The humanitarian consequences are severe and likely to persist for months or longer. At least 28 health facilities in Jonglei were damaged or looted this year, with 70 percent no longer functioning. The UN-backed Integrated Phase Classification warns of famine risk across multiple counties, with more than 70,000 people already facing the highest possible severity of hunger. Nicholas Kerandi of the UN Food and Agriculture Organization said the impacts on food security and public health "are likely to persist through the remainder of the year and potentially beyond." Emmerson Gono, deputy head of mission for Doctors Without Borders, visited Lankien in April and observed that "anything that can support the life of human beings was deliberately destroyed."

The violence represents an escalation of tensions that began in 2025, when opposition leader Riek Machar, the first vice president, was arrested on charges of subversion—allegations he denies. Machar and President Salva Kiir had been on opposing sides during South Sudan's 2013-2018 civil war, which killed hundreds of thousands before a peace agreement brought them into a fragile unity government. The implementation of that agreement stalled amid delays in unifying armed forces and repeated postponements of elections. Following Machar's arrest, the government launched aerial bombardments against a simmering rebellion in rural areas. Machar's political group declared the peace deal dead and began launching attacks on military positions. What unfolded in Jonglei was the government's response—a counteroffensive that, according to residents and satellite analysis, left tens of thousands displaced and pushed the region toward famine. Ter Manyang Gatwech, a human rights advocate from Jonglei, told Al Jazeera that the alleged abuses have fractured trust across every level of society. "The tribes don't trust one another, the citizens don't trust the government, and the government doesn't trust its citizens," he said. "Unless there is a miracle, South Sudan will disintegrate."