Kenya, 7 November 2025 - Efforts to enhance the efficiency and operational speed of the Port of Mombasa have been elevated following the launch of a strategic partnership between the Kenya Ports Authority (KPA) and the Kenya Revenue Authority (KRA).
The landmark collaboration seeks to ease persistent congestion, accelerate cargo clearance, and strengthen coordination among the various government agencies overseeing import and export operations at East Africa’s busiest seaport.
The formal agreement was signed at KPA headquarters in Mombasa, witnessed by representatives from the Executive Office of the President’s Council of Economic Advisors, signifying the national importance of the reforms.
The move marks a major step by the Kenyan government to streamline logistics and improve the movement of goods through the country’s most vital trade gateway, which also serves as the primary maritime access point for several landlocked nations across East and Central Africa.
Under the new framework, containerised cargo destined for Mombasa will be cleared at Container Freight Stations (CFSs), while cargo bound for Nairobi and other inland destinations will be transported via rail to the Nairobi Inland Container Depot (ICD). Containers heading to Uganda will be moved to the Naivasha Inland Container Depot (NICD) for clearance.
To further enhance efficiency, KPA and KRA have introduced a range of incentives. Affected customers will receive a 100 percent waiver on accrued storage and warehouse rent for long-stay cargo for 30 days, subject to submission of a waiver application. Shipping lines have also been directed to waive container detention and demurrage charges during this period.
However, primary port charges, rail freight fees, shipping line costs, and statutory taxes will continue to apply, the agencies clarified in a joint statement issued after a high-level meeting chaired by the Executive Office of the President and the Council of Economic Advisors at KPA headquarters.
KRA also announced measures to streamline cargo management, noting that it will determine which consignments qualify for auction and sustain gazette notices to enable importers to clear pending goods. Cargo approved for destruction will be transferred to licensed destruction facilities.
The agencies further stated that containers operating under the Single Customs Territory (SCT) regime will generally be exempt from e-seal arming processes, except in cases flagged through risk assessment.
In a statement released on Thursday, a list of 13 immediate actions has been outlined to reduce congestion, enhance operational efficiency, and modernize customs procedures at the Port of Mombasa. These measures form a comprehensive plan to tackle long-standing logistical bottlenecks that have hindered port operations.
According to the statement, cargo destined for Mombasa will be cleared through Container Freight Stations (CFSs). At the same time, shipments bound for Nairobi and other inland destinations will be transported by rail to the Nairobi Inland Container Depot (ICD) for clearance.
These initiatives come amid a decade of significant infrastructure investments in Kenya, including the Standard Gauge Railway linking Mombasa to Nairobi and extending toward Uganda, an upgrade intended to streamline cargo movement from the coast to the hinterland.
