Shockwaves at Mombasa: South Sudan’s New Container Levy Cripples Kenya–Juba Trade

When the memo first surfaced on 17 November 2025, it read like a commercial earthquake for the Mombasa–Juba corridor: a new charge of US$ 3,580 per container, around KSh 461,820, was to be imposed on all cargo destined for South Sudan.

The notice also scrapped the longstanding empty container deposit of US$ 5,000. The directive, attributed to South Sudan Revenue Authority (SSRA’s) Commissioner General William Kuol, landed abruptly in clearing and forwarding agents’ inboxes, without prior consultation or diplomatic notice.

Within days, Mombasa-based cargo handlers halted all South Sudan bound operations.

“We were shocked to get the communication from South Sudan Revenue Authority (SSRA) Commissioner General William Kuol even without consulting us,” said Roy Mwanthi, the agents’ representative in Mombasa.

“The removal of the fees is advantageous to South Sudan traders but puts shippers and clearing and forwarding agents at risk of losses since container return or in good condition is not assured,” added fellow agent John Mwangi.

As trucks sat idle and containers piled up, the optimism SSRA had offered in the notice, of streamlined cargo tracking, traceability via a mandatory “One-Time Password (OTP)” and reduced costs for South Sudanese traders, rang hollow for Kenyan agents footing the new levy burden.

Why Kenya Has a Lot to Lose

Kenya has long served as the key port gateway for South Sudan’s external trade.

The Port of Mombasa handles vast volumes destined for Juba, with numerous freight forwarders, container freight stations (CFS), trucking firms, insurers and exporters depending on the corridor for business continuity.

As a landlocked country, South Sudan’s reliance on over land supply chains through Kenya means any disruption to transit, especially one triggered by sudden levies, sends ripples across sectors.

For Kenyan clearing agents and exporters, the new levy is a blow to their bottom line and operational viability.

Many consignments carry goods like food staples, construction materials, consumer goods, and medical supplies, essential for daily life and commerce in Juba and beyond.

The imposition of $3,580 per container, on top of freight and logistics costs, risks pushing businesses into loss or abandonment of trade routes.

Nor is this the first time South Sudan has tried to restructure how cargo is taxed or tracked. The controversial Electronic Cargo Tracking Note (ECTN) levy of US$ 350 per container, previously imposed, triggered legal battles and court interventions when freight agents challenged it in Kenya.

A Rift in Trust, Procedure, Legitimacy and Cargo Ethics

The crux of the uproar is on the way the directive was issued. Agents say that instead of following established regional diplomacy or notifying stakeholders, the SSRA used informal channels, social media and direct memos, to announce a sweeping new levy. For them, that invalidates the directive’s legitimacy.

Former Kenya International Freight and Warehousing Association (KIFWA) chair and veteran agent Roy Mwanthi told journalists that the levy was “punitive” and contradicted the normal protocol:

“We are being told the government of South Sudan wants to collect 3,580 dollars from shippers on containers they do not own. That is not their business.”

Some agents argue that containers should not be treated like pawns: many of the containers heading to Juba are owned by the importers or shipping lines, yet the levy treats them uniformly as if belonging to SSRA. For agents and transporters, the lack of a container return guarantee increases risk dramatically.

From the SSRA side, the policy was presented as a reform, one they say aims to strengthen cargo tracking through an e portal, requiring a “Maritime Container Release One-Time Password (OTP)” for any container exiting the Port of Mombasa bound for South Sudan. The abolition of the old empty container deposit was intended to lower barriers for South Sudanese traders and encourage increased cargo volume.

Yet the opacity surrounding the directive’s origin, and the sudden enforcement, left many in the regional logistics community feeling blindsided.

Suspended Cargo, Idle Assets and Regional Disruption

The result was swift. Clearing and forwarding agents at Mombasa suspended all services for South Sudan bound cargo, effectively grinding traffic to a halt. Trucks remain parked, container freight stations are overflowing, and goods bound for Juba, ranging from food to building materials, are stuck in limbo.

For Kenyan exporters, logistics firms, and transporters, the suspension translates into lost revenue, idle labour, demurrage charges, and potentially broken contracts. For South Sudanese importers, especially those relying on timely delivery of essentials, the disruption threatens supply shortages and inflated prices.

Industry insiders now warn that if the directive remains unchanged, the Mombasa–Juba corridor may permanently shrink, pushing importers to seek alternate, less reliable trade routes, or worse, stimulating informal, untracked smuggling and black market channels.

What’s at Stake

Regional stability & economic interdependence, Kenya and South Sudan are economically intertwined; trade disruptions hurt not just exporters, but communities that depend on affordable goods, imports and imports-based livelihoods.

Trade predictability & investor confidence, Frequent unilateral levies undermine trust in the corridor’s reliability. Investors and businesses need stable, predictable trade rules to plan supply chains.

Governance, transparency and diplomacy, the manner in which the SSRA issued the directive, reportedly via social media and memos, raises questions of process, legitimacy and use of proper inter state channels before imposing major levies.

Human costs, the ripple effects, of halted goods, delayed medical supplies, construction materials, consumer goods, could amplify hardship in South Sudan, a country already vulnerable due to conflict, instability and economic fragility.

What Needs to Happenn and What to Watch

Formal diplomatic engagement: Kenyan authorities, including the Ministry of Transport and foreign relations offices, must demand the original SSRA directive and engage Juba in talks. Freight stakeholders calling for clarity, not confrontation, should be heard.

Public release of directive: SSRA needs to publish the full notice (or memo), showing exactly what the levies, exemptions, container return policies and OTP systems entail. This transparency is key for trust.

Contingency trade routes & risk mitigation: Kenyan exporters and logistics firms should evaluate alternate routes (if any), insurance, and contract clauses to avoid exposure. Regional bodies like the East African Community (EAC) could mediate or propose frameworks to avoid unilateral shocks.

Media and public scrutiny: Investigative coverage to trace cargo currently stuck, losses incurred, and human level impacts (traders, retailers, consumers), to pressure policymakers for a swift, fair resolution.

What began as a technical directive, a container levy and new tracking protocol, has spiralled into a full blown trade crisis.

For Kenya, the risk is not just financial loss, it’s the erosion of trust in regional trade, the potential breakdown of logistics networks, and the displacement of livelihoods tied to cross border commerce.

For South Sudan, the levy’s shockwaves could deepen shortages, raise costs for consumers, and further destabilise an already fragile economy.

As the Port of Mombasa quiets and trucks idle in silence, one thing is clear: without transparency, consultation, and regional solidarity, corridors meant to connect nations will continue to divide them, cargo by cargo.

Source: https://www.dawan.africa/news/shockwaves-at-mombasa-south-sudans-new-container-levy-cripples-kenya-juba-trade