The Kenya Ports Authority (KPA) and the Kenya Revenue Authority (KRA) have entered into a joint agreement aimed at accelerating cargo clearance, easing congestion, and enhancing efficiency at the Port of Mombasa.
The pact, signed at KPA headquarters in Mombasa and witnessed by the Executive Office of the President’s Council of Economic Advisors, outlines coordinated short and medium-term measures to streamline operations, reduce dwell time, and strengthen inter-agency collaboration.
Other stakeholders, including representatives from KeBS, KR, KEPHIS, KSAA, SCEA, KIFWA, KTA, CFSA, and CMA, were also present, signalling a renewed government push to decongest the port and enhance trade facilitation along regional logistics corridors
A communiqué issued after the signing outlines 13 key interventions aimed at easing congestion, cutting turnaround time, and modernising customs and port procedures.
This initiative aims to enhance Kenya's competitiveness and position the Port of Mombasa as the most efficient maritime hub in East and Central Africa.
Effective immediately, all long-stay containerised cargo at the port will be moved to customs-licensed peripheral facilities.
“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),” it states.
Cargo bound for Uganda and other regional markets will now be relocated to the Naivasha ICD for clearance.
To encourage the evacuation of long-stay cargo, both KPA and KRA will waive 100% of accrued storage and warehouse rent for affected importers, provided applications for waivers are lodged within 30 days.
Shipping lines have been urged to complement this exercise by waiving container detention and demurrage charges, while statutory port fees, rail freight, and taxes will remain payable.
KRA will also fast-track auction processes for unclaimed cargo, sustain gazettement of consignments pending clearance, and ensure that goods earmarked for destruction are moved to licensed destruction 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,” reads the communique.
To enhance logistics and truck turnaround time, KRA and KPA will implement risk-based scanning procedures, allowing containers bound for CFSs to be transferred immediately after scanning, with image analysis completed later.
Kenya Railways is set to provide a detailed shunting schedule to improve traffic flow, while Port Police, KPA, and KR will jointly ensure intersections remain clear.
KRA will also geofence Gate 24 to facilitate transit cargo exit, complementing Gates 18 and 20.
The communiqué underscores the need for round-the-clock port operations, harmonising agency working hours to ensure seamless 24/7 processing.
It states that cargo not cleared within the five-day free storage period will be transferred to nearby CFSs, with importers allowed to nominate their preferred station.
Additionally, KRA will roll out a Pre-Arrival Processing (PAP) system to allow documentation and clearance before cargo arrival, while long-term efficiency will be achieved through digital alignment across all port systems.
Speaking at the signing, KPA Managing Director William Ruto said the partnership marks “a new era of operational synergy aimed at reducing dwell time and ensuring Kenya remains a competitive gateway for regional trade.”
Representing the 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 remains a critical artery for regional trade, handling cargo for Uganda, Rwanda, Burundi, South Sudan, and the DRC.
The new measures are expected to reduce clearance time, cut costs, and attract more global shipping traffic as Kenya continues to modernise its logistics infrastructure.
