Xavier Radio Ug News 24 7
The escalating e-permit chaos between South Sudan and Uganda has now thrown the job of Uganda Revenue Authority (URA) Commissioner General John Musinguzi Rujoki into dangerous territory — with powerful groups allegedly pushing to bulldoze the new system through at all costs.
Insider sources say the people bankrolling the controversial South Sudan electronic import permit rollout are “ready to crush anyone” who stands in their way — including top revenue bosses in Kampala.
And now, a botched high-level emergency meeting between the two countries’ revenue chiefs has left traders stranded, borders confused, and accusations of a mafia-style scheme flying across East Africa’s busiest commercial corridor.
HOW THE CHAOS BEGAN
In September, the South Sudan Revenue Authority (SSRA) introduced mandatory electronic import permits for all goods entering the country via Uganda — its biggest trading partner.
URA was later notified, and both countries entered a loose, unclear agreement on November 17, 2025.
Then, on 20th November, SSRA Commissioner General William Anyuon Kuol issued a tough directive: No cargo destined for South Sudan will move without an e-permit. No exemptions except those personally issued by the SSRA Commissioner General. All exemptions must still be tracked on the regional RCTs system. All diverted cargo (e.g., goods meant for DRC but rerouted to South Sudan) must undergo e-permit revalidation. Any non-compliance will attract “administrative action”.
The circular was copied to high-ranking revenue bosses, signaling full enforcement.
URA PUSHES BACK
However, the URA Commissioner General has taken a lead in protecting both Ugandan and Sudanese traders by swiftly suspending the E-Permit enforcement for the destined goods to South Sudan due to predicted and detected adverse effects of the system. In a major trade escalation, the Uganda Revenue Authority (URA) has halted the strict enforcement of the regional e-permit system for all cargo destined for South Sudan, a day after Juba issued a sweeping directive demanding full compliance with the digital documentation regime.
In a memo dated 21st November 2025, addressed to the Assistant Commissioners for Enforcement and Border Control, the URA’s Customs Compliance Division announced an interim suspension of e-permit enforcement, citing widespread trade disruptions and inconsistencies triggered by South Sudan’s earlier directive.
In its memo, URA acknowledges South Sudan’s right to implement the e-permit system but warns that the abrupt full enforcement “had reverse impacts on trade facilitation.”
URA cites several complications: Multiple exemptions issued from South Sudan that caused non-uniform implementation. Lack of a clear exclusion procedure for exempt cargo. Some consignments not electronically tracked, yet being subjected to mandatory e-permits. Generalized application of the new rule creating confusion and congestion along transit routes and risk of compromise to electronic sealing procedures within the regional RCTs tracking system.
The memo notes that the fallout had already begun to hurt manufacturers, exporters, and other trade actors within the import–export value chain.
To avert what URA describes as a “current crisis,” the authority has: Suspended the e-permit enforcement for South Sudan-bound cargo. The taxman has hence ordered that the e-permit system be disabled from the RCTS tracking platform to avoid further disruptions. URA says the suspension is temporary, pending bilateral engagement with the South Sudan Revenue Authority to agree on a “clear way forward.
The contradictory directives have created confusion among transporters, clearing agents, and exporters who handle large volumes of goods bound for South Sudan—Uganda’s second-largest export destination in the region.
Whereas South Sudan insists on strict digital monitoring to curb smuggling and revenue loss, URA argues that enforcement must be phased and coordinated to prevent supply chain paralysis.
KAMPALA CRISIS MEETING COLLAPSES
Amid the turmoil, SSRA boss William Anyuon Kuol planned to make an impromptu and unscheduled trip to Kampala for emergency talks on Saturday, 22nd November. However, sources confirm the meeting never happened — under unclear and murky circumstances.
Details, which we shall reveal in our subsequent publication will shock the trading community.
THE WIDER PLOT: WHO IS BEHIND THE E-PERMIT PUSH?
Highly connected South Sudan–linked company Crawford Capital Ltd is being whispered as the hidden hand behind the e-permit rollout.
Its motives remain unclear, but traders and civil society claim the system appears designed to ‘extract’ money, not to facilitate trade.
Sources claim powerful individuals in Kampala—with influence strong enough to trigger reshuffles at URA—are reportedly working behind the scenes pushing for the system’s adoption — even if it destabilizes regional trade.
This raises uncomfortable questions: Are private interests driving national revenue policy? Why are non-ministerial officials issuing directives with regional impact? Are traders being exposed to double taxation and unofficial fees?
Traders at Elegu–Nimule report being forced to buy electronic permits even after paying official customs duties.
Some receipts allegedly lack government(s) coding, raising fears that millions may be diverted into private accounts instead of national treasuries.
A regional economist has since warned: “South Sudan’s economy is fragile. Any unmonitored extractions directly undermine revenue and inflate market prices.”
Ugandan enforcement officers, meanwhile, are said to be operating under ambiguous or unofficial directives, risking Uganda’s compliance with EAC trade protocols.
REGIONAL TRADE AT RISK
The unending saga has already triggered: Costly delays along the Elegu–Nimule corridor. Rising commodity prices in Juba. Confusion among drivers, clearing agents, and cargo owners. Growing suspicion of a revenue coup by private actors. Potential breaches of EAC trade agreements.
Business associations warn that the new electronic system is not anchored in regional frameworks and is creating a non-tariff barrier disguised as modernization.
CALLS FOR FULL INVESTIGATION
Civil society, traders’ unions, and logistics associations are demanding answers on: The legal mandate for the electronic permit system. Who exactly is the private company involved and to what extent? Where do the collected fees go? Why Uganda is enforcing a system not recognized under EAC rules? Whether officials in both countries are fronting the scheme for private enrichment.
With South Sudan being Uganda’s largest regional trading partner, hundreds of trucks remain stuck, and uncertainty continues to deepen.
The question hanging in the air: Is the e-permit system genuine modernization — or a cross-border cash-harvesting cartel?
And more pressing: Will URA CG Rujoki survive the escalating power games behind the scenes?
About Post Author
Post navigation
