Cargo containers at the Port of Mombasa.
The taxman has deferred a scheduled shutdown of its cargo clearance system, bowing to pressure from traders, shipping companies and clearing agents who have flagged risks of bigger disruption at the gateway, which has been battling a congestion crisis since 2025.
The Kenya Revenue Authority's (KRA) Integrated Customs Management System, which is a crucial platform for the clearance of import and export cargo, is scheduled to go offline from Saturday April 4, 2026 at 6pm until Monday April 6, 2026 at 6am to allow for maintenance.
Traders and clearing agents, however, expressed reservations about the scheduled shutdown, barely a month after a similar exercise triggered massive disruptions at the Mombasa port—forcing the KRA to reschedule maintenance works on iCMS.
“This rescheduling follows extensive stakeholder consultations and a strategic assessment of current operations at the Port of Mombasa. The decision underscores the collective commitment of all government Agencies and the business community to ensure the efficient, smooth evacuation and movement of cargo,” the taxman said.
KRA said that the iCMS would now be shut down for maintenance on April 12, 2026.
The iCMS involves submitting export or import documents into a single-window system and provides an efficient interface with the customs management systems of the EAC neighbours.
The postponed scheduled maintenance had triggered a scramble among traders and clearing agents who, in February, were hit by a shutdown of the system, which resulted in massive traffic gridlock at the gateway.
The downtime in February affected various users of the iCMS platform, including importers, exporters, clearing and forwarding agents, shipping lines, and some government agencies.
Before the disruptions in February, the Mombasa port had already been dealing with congestion due to high container volume and previous system bottlenecks. This prompted the KRA and the Kenya Ports Authority (KPA) to implement urgent remedial measures, including moving cargo that had stayed at the port for over 21 days to Container Freight Stations (CFSs) and transferring transit cargo to Naivasha Inland Container Depot for clearance.
As part of efforts to decongest the port, KPA also suspended the direct loading of empty cargo containers onto ships at Mombasa Port as part of desperate measures to help deal with rising congestion at the key gateway.
The port manager directed that all empty containers be held in intermediate storage depots for a mandatory 72 hours before being allowed into the port for loading onto ships to help deal with worsening congestion at the Mombasa port.
Usually, logistics teams are allowed to directly load empty cargo containers onto ships from storage depots to the terminal crane area for immediate loading, sidestepping the lengthy process of intermediate storage at the port.
Additionally, KPA allocated empty container space per berth, capped at 2,000-2,500 containers except Berth No. 20. For exporters, the agents were ordered to ferry the consignment into the Port 36 hours before berthing of the carrier vessel, and no vessel were planned for berthing unless the discharge list, export full loading list, and empty container loading list had been submitted and approved.
In the push to curb congestion, KPA also allowed empty containers delivered ex-Inland Container Depot for loading to stay up to a maximum dwell time of 24 hours at the Port Reitz offloading zone, and those exceeding the allocated dwell time were relocated at the full cost of the respective shipping line.
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