At least 500 trucks destined for South Sudan have been stranded at the Malaba border between Kenya and Uganda since March 30, due to a new requirement by Juba demanding upfront payment of e-permit taxes.

Transporters say some of the trucks carrying fuel, cement, food and World Food Programme supplies had already been delayed for more than two weeks.

They complain about emerging non-tariff barriers (NTBs) imposed by East African Community (EAC) member states, increasing the cost of doing business in the region.

Worse still, they cite eastern Congo, where at least 24 illegal roadblocks have been set up by militias and corrupt public servants who demand at least $300 per truck per roadblock.

Ahmed Farah, East African Business Council (EABC) chief executive singled out the Goli-Mahagi-Kisangani route in eastern DRC as one of the most expensive routes on the Northern Corridor.“These (roadblocks) are not minor inconveniences; they are market-closing instruments,” said Elias Baluku, executive director of the Federation of East African Freight Forwarders Associations, a regional private sector body of customs, clearing and freight forwarders.

“In the South Sudan case, previously, the e-payment taxes were processed at the Nimule border or in Juba, allowing goods to be cleared under bond. The shift in enforcement to the point of origin has led to significant disruption, resulting in congestion of over 500 trucks at the Malaba border.”Malith Jacob Apui, SSRA assistant commissioner in Nimule, downplayed the crisis, but Juba officials acknowledged that there was a problem at the Malaba border.“We spoke with officials in Juba,” Mr Baluku said. “The issue is South Sudan, as a precautionary step, decided to enforce the requirement by the Single Customs Territory (SCT) for goods to be cleared at the first point of entry, so that is what they are trying to enforce, likely informed by fears of cargo diversion.“When we asked why they were doing this they said it is to ensure that anybody who says that the cargo is going to South Sudan could then pay South Sudanese Customs what is due to them.”Under a Single Customs Territory (SCT), internal border controls are minimised to allow free circulation of goods. Goods are cleared once at the first point of entry, with taxes paid at the destination country.“South Sudan has not yet fully incorporated the Customs Union requirements and that is where the challenge is,” Mr Baluku noted.

Apart from the trucks logjam at the Malaba border, South Sudan is charging a $40 weighbridge service fee per truck that crosses at Nimule. In the event of having an overload, they negotiate a fee between $600 and $2,500.

”The Trade Barriers Organisation March 2026 report shows 95 unresolved NTBs across the EAC-Comesa-SADC area. This is despite the EAC Heads of State Summit having set June 2026 as the deadline for the end of non-tariff barriers.“The private sector needs certainty. Traders require predictability. Investors seek stability. Without stronger political resolve, the gains achieved through infrastructure investments, customs reforms, digitalisation and corridor improvements risk being gradually reversed,” said Allen Sophia Asiimwe, deputy CEO and Chief of Programmes at TradeMark Africa.

In Congo, Mahagi (DRC)/Goli (Uganda) is one of the busiest border crossings, at the axis linking the popular centres of Arua (Uganda), Bunia (DRC), Kisangani (DRC) and the port of Mombasa on the Northern Corridor.

The DRC remains a top export market for neighbouring countries like Uganda, yet these barriers threaten to reduce trade volumes.

The increased NTBs in DRC are affecting trade volumes between Uganda and DRC, which are poised to surpass the record $1 billion total recorded in the 2024–2025 financial year, largely driven by Uganda's increasing exports of refined vegetable oil, sugar, and industrial goods to the eastern Congo region.

According to active complaints reported on Tradebarriers.org, Rwanda has introduced a 39 percent excise duty on juice manufactured in Kenya, violating the EAC Common Market Protocol.

Tanzania imposed a 10 percent excise duty on detergents from Kenya, violating the principles of the EAC Protocol Articles 15 & 75 and creating an unfair competitive environment.

In Kenya, Kajiado County has been reported for charging transit fees of $15.5 (KSh 2,000) per foreign transit truck. Rwanda is charging $270 from Rusumo border to Kigali, which is equivalent to $80.83 per 100km, while Tanzania is charging $10 per 100km. This is against the agreed principle of distance x weight for transit vehicles.

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