(JUBA) – South Sudan has closed an Egyptian military facility in the Pagak area of Upper Nile State near the Ethiopian border, a move that signals a major shift in regional alliances linked to the River Nile, oil exports and security cooperation in East Africa.
The closure marks a setback for Egypt’s long running strategy of maintaining influence around Ethiopia as tensions continue over the Grand Ethiopian Renaissance Dam, commonly known as GERD. The military station in Pagak had operated since 2020 and reportedly hosted about 260 Egyptian personnel including trainers, technicians and logistics officers.
Reports indicate that Egyptian President Abdel Fattah al Sisi held a private meeting with senior military and intelligence officials in Cairo on 2 June after learning that South Sudan had decided to end the Egyptian military presence in the area.
The Pagak facility was strategically important for Egypt because of its location near Ethiopia’s Benishangul Gumuz region where the GERD project is based. Cairo viewed the base as an important intelligence and surveillance point during years of disagreement with Addis Ababa over Nile water management and the future operation of the dam.
Diplomatic tensions between Egypt and South Sudan had reportedly increased in recent weeks before the closure. In mid May, Egyptian officials summoned South Sudan’s ambassador in Cairo to communicate concerns over Juba’s decision to terminate the military arrangement.
The development comes at a time when regional political and economic alliances are changing rapidly across the Horn of Africa and the Nile Basin. Analysts say South Sudan’s decision reflects growing economic pressure on Juba and a stronger need to cooperate with neighbouring Ethiopia on trade and energy infrastructure.
South Sudan remains heavily dependent on oil exports for state revenues. More than 90 per cent of the country’s crude oil exports currently move through pipelines crossing Sudan to Port Sudan on the Red Sea. However, the ongoing conflict in Sudan between the Sudanese Armed Forces and the Rapid Support Forces has disrupted trade routes, damaged infrastructure confidence and reduced government income in Juba.
Faced with these pressures, South Sudan has increasingly explored alternative export and transport routes through Ethiopia. Attention has focused on the Gambela Pagak corridor, which is viewed as a possible future route for oil exports and regional trade links.
The closure of the Egyptian base also reflects wider political changes in Nile Basin cooperation. At the end of 2024, South Sudan joined Ethiopia, Uganda, Tanzania, Rwanda and Burundi in signing a framework agreement on Nile Basin cooperation. Egypt and Sudan have opposed the agreement because they believe it weakens earlier arrangements that historically gave Cairo and Khartoum dominant rights over Nile waters.
Under agreements signed in 1929 and 1959, Egypt receives an annual allocation of 55.5 billion cubic metres of Nile water. Ethiopia has long argued that these agreements are outdated because most of the Nile’s water originates outside Egypt, particularly from the Ethiopian highlands.
For South Sudan, the latest developments show how economic needs are increasingly shaping foreign policy decisions. Juba’s growing interest in alternative oil corridors, regional trade access and new infrastructure partnerships appears to be influencing its diplomatic position within the Nile Basin.
The closure of the Pagak base may also affect future security cooperation between South Sudan and Egypt. In recent years, Egypt had gained military access to several South Sudan locations including Bor, Pibor, Pochalla, Paloich and Malakal following broader financial and infrastructure cooperation linked to loans and investment arrangements.
While neither government has publicly outlined the next stage of relations, the decision illustrates how shifting trade realities, oil export risks and regional security concerns are changing alliances across East Africa.