MOMBASA, Kenya, November 11, 2025 — The Kenya Ports Authority (KPA) and the Kenya Revenue Authority (KRA) have signed a joint communiqué outlining a raft of measures aimed at enhancing efficiency and trade facilitation at the Port of Mombasa.
The agreement was reached following a meeting chaired by the Executive Office of the President’s Council of Economic Advisors at the KPA headquarters in Mombasa. The session brought together key port stakeholders, among them the Kenya Bureau of Standards (KEBS), Kenya Railways (KR), Kenya Plant Health Inspectorate Service (KEPHIS), Kenya Ship Agents Association (KSAA), Shippers Council of Eastern Africa (SCEA), Kenya International Freight and Warehousing Association (KIFWA), Kenya Transporters Association (KTA), Container Freight Stations Association (CFSA), and the Capital Markets Authority (CMA).
Under the new measures, all long-stay containerised cargo at the Port will be transferred to customs-licensed peripheral facilities to decongest the terminal and facilitate faster clearance. Cargo destined for Mombasa will be moved to Container Freight Stations (CFSs) for final clearance, while upcountry-bound shipments will be transported by rail to the Nairobi Inland Container Depot (ICD). Cargo destined for Uganda will be transferred to the Naivasha ICD for clearance by customers.
In a bid to encourage the evacuation of containerised cargo, KPA and KRA will waive 100 percent of accrued storage and warehouse rent for long-stay cargo upon application by affected customers for a period of 30 days. Shipping lines have also been directed to waive container detention and demurrage charges to ensure the success of the exercise. However, all primary port charges, rail freight fees, shipping line costs, and statutory taxes will remain payable.
KRA will determine all cargo that qualifies for auction and ensure sustained gazettement of the consignments to allow importers an opportunity to clear their goods before auction. Approved cargo for destruction will be moved to licensed destruction sites, while all cargo operating under the Single Customs Territory (SCT) regime will be exempted from RECTS e-seal arming processes, except for specified cases based on risk assessment.
In an effort to reduce truck turnaround time, KRA will undertake risk-based scanning for transit cargo. Containers bound for CFSs will be scanned once and immediately transferred to respective facilities, with cargo image analysis and iScan messages sent thereafter.
To improve traffic flow within the Port, Kenya Railways will provide shunting schedules, while Port Police, KPA, and KR will work together to ensure intersections remain free from truck or rail wagon obstructions. KRA will also geofence Gate 24 to allow the exit of transit cargo, complementing the existing Gates 18 and 20.
The two agencies also committed to ensuring seamless 24-hour operations at the Port by harmonizing working hours and shift management among all cargo interveners. Domestic containerized cargo that is not cleared within the five-day storage period will be moved to CFSs, with importers encouraged to nominate their preferred stations. In cases where no nomination is made, KPA will assign the cargo to a CFS near the Port.
Partner Government Agencies (PGAs) will undertake all container interventions outside the Port in line with government directives on multi-agency interventions, ensuring that all issues are resolved within five days. KRA will also implement the Pre-Arrival Processing (PAP) of cargo to further expedite clearance.
In the medium term, the government has outlined plans to align policy actions and accelerate system digitization to deliver long-term efficiency and maintain the Port of Mombasa as the region’s preferred logistics hub.
The communiqué was signed by KPA Managing Director Capt. William Ruto and Dr. Lilian Nyawanda, representing the Commissioner General of KRA.
