E-Permit Confusion Disrupts South Sudan Markets

(JUBA) – The controversy over South Sudan’s electronic import permit (e-permit) system has intensified following the release of an internal memo from the Uganda Revenue Authority (URA) suspending its enforcement. The memo, dated 21 November 2025 and bearing the name of URA Commissioner Customs Asadu Kigozi Kisitu, is now under investigation after officials suggested it may have been issued without authorisation and possibly forged by a junior staffer.

The memo instructed URA staff to halt enforcement of the e-permit requirement for goods destined for South Sudan. However, insiders insist that Kisitu did not authorise the directive, raising concerns about possible internal sabotage and a wider cross-border revenue dispute.

The situation has put strain on Uganda–South Sudan trade and has placed the position of URA Commissioner General John Musinguzi Rujoki under scrutiny. Sources indicate that the stakeholders behind the e-permit rollout are determined to enforce the system, even against top Ugandan tax officials. The resulting confusion has delayed border operations, leaving traders and cargo stranded along the region’s busiest trade route.

The e-permit system was introduced by the South Sudan Revenue Authority (SSRA) in September 2025. URA initially recognised the system on 17 November, but the following day SSRA Commissioner General William Anyuon Kuol issued a directive insisting that no cargo enter South Sudan without an e-permit, with exemptions strictly controlled and tracked in the regional customs system.

URA’s controversial memo, which appeared on 21 November, cited several reasons for suspending enforcement, including non-uniform implementation of exemptions, unclear procedures for exempt cargo, and the risk of disruption in the regional customs tracking system (RCTS). The memo called for a pause in e-permit functions until further bilateral consultations.

Traders have expressed confusion as Uganda signals suspension while South Sudan maintains strict enforcement. An emergency meeting in Kampala on 22 November, involving SSRA leadership, reportedly collapsed under unclear circumstances.

Concerns are growing over the system’s design, with some observers claiming it prioritises revenue extraction over trade facilitation. Reports suggest that payments may have been diverted into private accounts and that some enforcement officers were operating under unofficial instructions, resulting in duplicate charges for traders.

The unfolding crisis has already caused major delays on the Elegu–Nimule corridor, higher prices in South Sudanese markets, and congestion for transporters and clearing agents. Economists and trade bodies warn that the system, which lacks East African Community recognition, could amount to a disguised non-tariff trade barrier and may undermine the fragile South Sudanese economy.

Traders, civil society, and logistics associations are calling for clarity on the legal basis of the e-permit, the role of private companies in its rollout, and the destination of collected funds. With hundreds of trucks stranded at the border, the situation remains tense and uncertain for the region’s trade.