A major effort is underway to further streamline cargo operations at the Port of Mombasa as key stakeholders in the port ecosystem agree to embrace reforms as part of turning the harbor into East Africa's logistics hub. 

In an update to the public, the Kenya Revenue Authority (KRA) in collaboration with the Kenya Ports Authority (KPA) and other cargo trade stakeholders has announced the roll out of reforms aimed at decongesting the Port of Mombasa while significantly improving efficiency.

In a statement, the agencies said the reforms are designed to help reduce cargo dwell time at the port while accelerating the clearance of goods through a tech-powered system. 

Speaking during the announcement of the reforms last week, KRA Commissioner-General Humphrey Wattanga said the shift mark a strategic move towards a more predictable, efficient and digitally enabled port ecosystem that better supports trade and regions economic growth. 

“The Port of Mombasa is not only a national asset but a critical regional gateway. Our objective is to eliminate bottlenecks, reduce cargo dwell time and build a predictable, efficient and digitally enabled clearance system that supports trade and economic growth,” said Wattanga while chairing a high-level stakeholders’ meeting on port reforms.

The forum was also attended by KPA Managing Director Capt. William Ruto and brought together key players in the maritime and logistics ecosystem, including transporters, shippers, freight forwarders, ship agents, and regulators.

Capt. Ruto reaffirmed KPA’s commitment to implementing the agreed measures in close partnership with KRA and industry stakeholders, noting that efficiency at the port is a shared responsibility.

"These reforms will unlock capacity, improve operational flow and strengthen Mombasa’s competitiveness as a regional and global port. KPA will dedicate the necessary infrastructure and resources to ensure their successful implementation,”Capt. Ruto said in a statement. 

As an urgent intervention to ease congestion, stakeholders resolved that all long-stay consignments earmarked for auction or destruction will be transferred to designated Container Freight Stations, beginning with cargo that has remained at the port beyond 21 days. 

The evacuation exercise will start at the G-section of the port and is expected to rapidly free up critical yard space, easing congestion and improving operational flow. 

To further accelerate clearance, KRA will expand the Pre-Arrival Processing framework, with priority given to bulk cargo, low-risk shipments, and Authorized Economic Operator consignments. 

The enhanced system will allow cargo to be processed before arrival, significantly reducing clearance times, improving predictability, and minimising delays. 

To address persistent shortages of Regional Electronic Cargo Tracking System (RECTS)seals, KRA will introduce a multi-vendor model through an open expression of interest process. 

This approach is expected to strengthen system resilience, ensure uninterrupted cargo tracking, and eliminate disruptions associated with seal shortages. 

In addition, KRA and KPA will engage the Kenya Railways Corporation to deploy additional wagons on the Standard Gauge Railway (SGR), accelerating the transfer of cargo to the Embakasi and Naivasha Inland Container Depots. This is expected to reduce pressure on the port and key road corridors while improving cargo evacuation timelines.

Stakeholders also agreed to increase the utilisation of Lamu Port for transhipment cargo to ease pressure on Kilindini and unlock the full potential of Kenya’s northern maritime gateway.

KPA has committed to dedicating adequate infrastructure and operational resources to support transshipment activities at Lamu. 

To address inefficiencies in the handling of empty containers, KPA has allocated a dedicated site within the port for stacking and loading empty units. 

Additionally, a new industry framework on empty container management will take effect from 26th January, 2026, and is expected to improve coordination and turnaround times. 

The reforms will be supported by deeper digital systems integration to eliminate multiple documentation requirements, reduce manual processes, and enhance operational efficiency. 

KRA will also deploy additional personnel at RECTS offices and port gates to speed up cargo arming and exit processes, delivering immediate gains in output and service quality. 

The coordinated reforms signal a strategic reset of Kenya’s port operations and are expected to significantly reduce cargo dwell time, improve clearance predictability, and strengthen Kenya’s position as East Africa’s premier logistics centre.

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