Kenya has unveiled a new plan to make the Port of Mombasa faster and more efficient through a partnership between the Kenya Ports Authority (KPA) and the Kenya Revenue Authority (KRA).
The deal is expected to ease congestion, speed up cargo clearance, and strengthen coordination between government agencies handling imports and exports.
The agreement was signed at the KPA headquarters in Mombasa in the presence of the Executive Office of the President’s Council of Economic Advisors.
It marks a major step by the government to improve how goods move through the country’s busiest seaport, which serves as a gateway for trade across East and Central Africa.
Officials from several key institutions also attended the signing, including the Kenya Bureau of Standards (KeBS), Kenya Railways, Kenya Plant Health Inspectorate Service (KEPHIS), Kenya Ships Agents Association (KSAA), Shippers Council of Eastern Africa (SCEA), Kenya International Freight and Warehousing Association (KIFWA), Container Freight Stations Association (CFSA), and the Capital Markets Authority (CMA). Their participation reflects a broader effort to unite all port stakeholders under one coordinated system.
A statement released on Thursday, November 6, 2025, detailed 13 actions that will be implemented immediately to reduce congestion, improve efficiency, and modernise customs procedures. Among the most significant measures is the relocation of long-stay containerised cargo from the main port to licensed customs facilities outside the port.
“Cargo destined for Mombasa will be transferred to Container Freight Stations (CFSs) for clearance, while that headed to Nairobi and upcountry regions will be railed to the Nairobi Inland Container Depot (ICD),” the statement read in part.
Cargo meant for Uganda and other countries in the region will now be cleared at the Naivasha ICD.
To support the exercise, KPA and KRA will offer a 100 per cent waiver on accrued storage and warehouse rent for importers who apply for relief within 30 days. Shipping lines have been encouraged to waive container detention and demurrage charges, although statutory fees, taxes, and rail freight charges will still apply.
The notice also said KRA will speed up the auctioning of unclaimed goods and continue publishing gazette notices for consignments pending clearance.
Goods marked for destruction will be moved to authorised facilities for proper disposal.
“All cargo cleared under the Single Customs Territory regime will be exempted from RECTS e-seal arming, except for consignments flagged through risk assessment,” it adds.
The agencies also plan to improve scanning procedures to allow containers heading to CFSs to be transferred immediately after scanning. Image analysis will be completed later, a move expected to save time while maintaining effective monitoring.
Kenya Railways will create a detailed schedule for shunting operations to improve traffic flow, while Port Police, KPA, and KR officers will work together to ensure intersections remain clear.
KRA will also introduce geofencing at Gate 24 to make it easier for transit cargo to exit, complementing the existing operations at Gates 18 and 20.
The statement also emphasised the need for continuous operations at the port, with all agencies harmonizing their working hours to support 24-hour service.
Cargo that remains uncleared beyond the five-day free storage period will be moved to nearby CFSs, with importers allowed to choose their preferred facility.
KRA is also preparing to roll out a new Pre-Arrival Processing (PAP) system, which will allow documentation and clearance to be done before cargo arrives in the country. In the long term, the agencies will integrate all port systems to allow for digital coordination and faster data sharing.
KPA Managing Director William Ruto said the new partnership marks “a new era of operational synergy aimed at reducing dwell time and ensuring Kenya remains a competitive gateway for regional trade.”
Representing KRA Commissioner General, Lilian Nyawanda said the measures will “enhance transparency, speed, and coordination between government agencies and the private sector, while supporting national revenue and trade facilitation goals.”
The Port of Mombasa is one of the most important economic facilities in the region, serving as a key trade route for Uganda, Rwanda, Burundi, South Sudan, and the Democratic Republic of Congo. The new measures are expected to cut costs, shorten clearance time, and attract more global shipping traffic as Kenya continues to invest in modernising its transport and logistics infrastructure.
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