Kampala, Uganda | THE INDEPENDENT | Uganda’s lucrative export corridor to South Sudan is facing fresh turbulence after some 1,000 trucks were stranded at Nimule border, following the introduction of a new electronic permit levy by the Government of South Sudan.
Appearing before Parliament’s Public Accounts Committee (PAC) on Thursday, 26 February 2026, officials from the Ministry of East African Community Affairs described the situation as a “serious disruption” to cross-border trade, warning that the levy of between $500 and $1,000 a truck, has triggered a near standstill in exports to Juba and driven up commodity prices in South Sudan’s capital.
The meeting was convened to scrutinize the Auditor General’s 2024/2025 report, but turned into heated quizzing over what MPs termed a “trade emergency.”
Leo Kizito Ojara, Commissioner for Economic Affairs at the ministry, told the committee that the newly introduced e-permit requires payment for each truck or container entering South Sudan from Uganda.
“For the last couple of weeks, there has been an introduction of a new tariff by South Sudan called an e-permit,” Ojara said. “You find one truck, one container, is expected to pay between 500 and 1,000 US dollars. The payment is excessive.”
According to the ministry, the levy has left over 1,000 trucks stranded at the Nimule border, a critical artery for Uganda’s exports to South Sudan, its largest regional market.
Uganda has consistently ranked South Sudan among its top export destinations, particularly for foodstuffs, construction materials, manufactured goods and fuel. Any prolonged disruption at Nimule, analysts warn, risks cutting into export earnings, destabilizing supply chains, and worsening inflation in South Sudan.
Ojara told MPs that prices in Juba have already spiked, citing sugar retailing at between UGX 10,000 and UGX 15,000 per kilogramme due to shortages linked to the stalled trucks.
“There is a big problem at the border as supplies to Juba are in shortage,” he said, calling for high-level diplomatic intervention. “In my view, we need a political solution. How quickly can you involve the Head of State in this matter? He should talk to his counterpart across the border.”
Permanent Secretary Edith Mwanje echoed the concern, warning that trade flows had slowed dramatically. “We’re deeply concerned about the impact on trade and the economy, the tax is crippling trade and pushing up prices of essential goods in Juba,” she said.
PAC Chairperson Gorreth Namugga described the levy as a major obstacle to regional integration, arguing that it undermines the spirit of the East African Community (EAC) Common Market Protocol, which guarantees the free movement of goods and services among partner states.
“This is a serious issue affecting our trade and economy,” Namugga said. She faulted the ministry for failing to promptly communicate the crisis to exporters, noting that many traders were still dispatching trucks to Nimule unaware of the standoff, thereby risking avoidable losses.
“Some trucks are stuck at the border, but others may still be packing items to go there. In such circumstances, how do we communicate so that we help people to avoid losses?” she asked.
The Auditor General’s report had already flagged weaknesses in communication and visibility of the ministry’s services, a concern Namugga said appeared unresolved.
Elijah Okupa (Kasilo County) urged swift action, particularly for traders dealing in perishable goods vulnerable to spoilage.
The standoff comes at a delicate time for regional integration efforts. The committee also discussed delayed subscription payments by partner states to the East African Community and ongoing consultations on the draft EAC Political Confederation Constitution, seen as a step toward deeper federation.
Under the EAC Treaty and the Common Market Protocol, partner states are expected to eliminate non-tariff barriers and promote seamless trade. Unilateral levies that significantly raise the cost of entry risk being classified as non-tariff barriers, potentially triggering formal dispute resolution mechanisms in the bloc.
Trade experts note that persistent barriers at key crossings like Nimule could erode business confidence and weaken the region’s push toward a confederation.
Citing the Auditor General’s findings, Namugga accused the ministry of underperformance.
“When you look through the Auditor’s report, it implicates you; it shows as if you are doing a lot of nothing,” she charged. “This is unacceptable. I want to express our disappointment and displeasure in the way you have appeared today!”
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