(MOMBASA COUNTY) – Cargo handling services for goods headed to South Sudan through the Port of Mombasa have been suspended after clearing and forwarding agents protested against a new charge introduced by the South Sudan Revenue Authority.
Agents say they were taken by surprise when a new fee of $3,580 (about 25,318,000 SSP) per container was introduced without consultation. They argue that the decision affects all shippers, clearing firms and transporters involved in moving cargo to South Sudan.
Roy Mwanthi, speaking on behalf of the Mombasa agents, said they were not informed before the announcement was made. “We were shocked to get the communication from South Sudan Revenue Authority commissioner general William Kuol even without consulting us,” he said.
A notice issued on 17 November 2025 confirmed the new fee and also removed the existing container deposit charge of $5,000 (about 35,500,000 SSP). The deposit has long been used as security to ensure containers are returned once unloaded in South Sudan.
Many traders and shipping agents say containers destined for Juba often fail to return, and the deposit is used to cover these losses. Removing it, they argue, exposes them to financial risks.
John Mwangi, a Mombasa based clearing agent, said the decision works against the interests of those responsible for shipping assets. “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,” he said.
| Item | Previous Fee | New Fee / Status | Equivalent in SSP | Notes |
|---|---|---|---|---|
| South Sudan Cargo Handling Fee | Not applicable | $3,580 | 25,318,000 SSP | Introduced per container without prior consultation; agents suspended services |
| Container Deposit Fee | $5,000 | Removed | 35,500,000 SSP | Previously ensured container return; removal exposes shippers to potential losses |
| Cargo Volume | 1.5 million tonnes | No change | N/A | Targeted for growth through reduced costs, but suspension may affect throughput |
| Stakeholder Action | Normal operations | Service suspension | N/A | Mombasa clearing and forwarding agents halted services pending withdrawal or consultation |
| Government Directive | Manual processes | OTP via e-government portal | N/A | Aim to improve cargo management, reduce container loss, strengthen coordination |
South Sudan introduced the policy to make its trade more attractive by reducing business costs and increasing the volume of cargo passing through Mombasa, currently estimated at 1.5 million tonnes each year. However, handlers in Mombasa warn the move could lead them to avoid South Sudan cargo entirely, as many containers are never returned to Kenya.
Agents say the new fee is too high and will affect regional trade between Kenya and South Sudan. They now want the Kenyan government and regional authorities to intervene before the matter disrupts the wider transport and logistics network.
On Friday, the clearing and forwarding agents confirmed that the suspension of services will continue until the charge is withdrawn and formal consultations take place.
In the notice, commissioner general William Kuol directed all cargo handlers to obtain their OTP documents from the official government e-government platform. The directive aims to improve cargo management, reduce loss of containers and improve coordination with regional ports and shipping lines.
Mr Kuol said the policy reflects joint efforts between Kenya and South Sudan to ease costs for traders. “The decisive action undertaken jointly by the governments of Kenya and South Sudan to provide substantial relief to South Sudanese traders and signals a new era of regional cooperation,” he said.
Members of the South Sudan business community in Mombasa welcomed the removal of the container deposit fee, saying they have campaigned for a decade for its abolition. Emmanuel Kachuol, the group’s chairman, said improved tracking systems will ensure shipping lines are assured of the return of their containers.
“Finally, the exorbitant empty container deposit fee has been abolished. This prohibitive fee has been so high and negatively affected the entire business chain in South Sudan,” he said. “With the abolishment of the fees, South Sudan traders will be motivated to do business with Kenya due to low operation cost.”
Shippers, however, maintain that containers are expensive assets and that safety measures are necessary to protect them. They warn that the lack of a deposit system will expose businesses to significant losses and place long term pressure on logistics stability.
| Item | Previous Charge | New Charge | Equivalent in SSP |
|---|---|---|---|
| New South Sudan cargo fee | Not applicable | $3,580 | 25,318,000 SSP |
| Container deposit (abolished) | $5,000 | Removed | 35,500,000 SSP |
