(MOMBASA / JUBA) – Clearing and forwarding agents handling cargo destined for South Sudan at the Port of Mombasa have stopped their operations after a notice circulating on social media claimed that a new fee of 3,580 US dollars per container would be charged. The agents say the fee was introduced without consultation and does not follow the established regional procedures that govern trade within the East African Community.
The agents announced their suspension late on Friday after the unverified memo prompted concern among cargo handlers, transporters and logistics firms serving the Mombasa to Juba corridor. Jakony Media Agency could not confirm the authenticity of the memo.
Speaking to Kenyan media in Mombasa, former Kenya International Freight and Warehousing Association chair Roi Mwanthi said the directive came as a surprise to all stakeholders. He said it was issued through social media instead of official diplomatic channels and therefore should not be considered legitimate.
He said the single customs territory rules require commissioners of any member state to consult their counterparts before introducing new charges. According to him, this did not happen, and the lack of consultation has already affected business confidence among importers moving goods to South Sudan.
Mwanthi said importers buy the goods together with the containers they arrive in, and these should not be treated as separate items attracting new fees. He added that under normal practice, when a container deposit is paid, it is later refunded once the empty container is returned to Mombasa. The memo circulating online does not mention any refund arrangement, making it unclear how the money would be handled.
He said this would add to the cost of business in the region, especially for traders supplying the South Sudan market, where transport charges and port costs are already high.
According to him, other East African Community states do not impose such fees, and South Sudan appears to be the only country linked to the directive. He pointed out that importers who buy their own containers should be exempt from extra charges because the containers belong to them and not to shipping companies.
He accused some South Sudanese authorities of going beyond their mandate by seeking to collect money from containers they do not own. He called on all governments using the Port of Mombasa to respect regional protocols and ensure that any taxes or levies for South Sudan are collected at South Sudanese borders rather than at the port.
The dispute comes only weeks after the South Sudan Revenue Authority issued an official notice on 17 November 2025 removing the long standing container deposit fee of 5,000 US dollars. In the same notice, the authority introduced a Maritime Container Release One Time Password. The OTP is a digital code that must be generated through a government portal before cargo bound for South Sudan can be released. The Revenue Authority said the OTP would improve transparency and help in tracking containers.
However, clearing agents say the new 3,580 US dollar fee circulating online is not part of the official government directive. They say they do not know its origin and demand that it be withdrawn or clarified.
Mwanthi warned that the continued uncertainty has already disrupted operations at the port. He said clearing agents will not process any containers or loose cargo for South Sudan until the matter is formally addressed.
He called on both the Kenyan and South Sudanese governments to clarify the situation quickly and to consult stakeholders before introducing any new charges.
The suspension is expected to delay cargo deliveries to South Sudan at a time when traders are preparing for end of year supply movements.
