Kenya has reintroduced mandatory rail haulage of cargo from Mombasa port to inland destinations, citing severe congestion as parts of the facility remain disrupted.

The directive has revived opposition from transporters, who note that a similar order was quashed by the High Court in 2020. Since last Friday, truck movements have been suspended as the Kenya Revenue Authority (KRA) upgrades its systems, leaving long queues and prompting officials to prioritise rail transfers to the Naivasha Inland Container Depot (ICD) for cargo bound for Uganda, South Sudan, the Democratic Republic of Congo and Rwanda.

On Tuesday, KRA Commissioner-General Humphrey Wattanga said Naivasha ICD would be prioritised for long-haul cargo due to increased volumes at Mombasa.

Clearing and forwarding agents, alongside the Kenya Transporters Association (KTA), opposed any move to make Naivasha ICD mandatory. They argue it would be illegal, anti-competitive and damaging to businesses along the Mombasa–Malaba corridor.

He blamed congestion on poor planning and vessel scheduling rather than underuse of rail, warning that forced haulage would breach constitutional provisions and court precedent.“The current congestion is a result of poor planning, vessel scheduling failures and challenges in empty-container evacuation. Vessels are departing with sub-optimal loads because they cannot wait to load empties. These failures will not be resolved through forced diversion of transit cargo to Naivasha ICD,” Mr Wang’oo said.

Court orderIn November 2020, the High Court revoked a directive by the Kenya Ports Authority (KPA) and KRA requiring all cargo from Mombasa to Nairobi to be transported via the standard gauge railway (SGR). A five-judge bench ruled that the order violated Articles 10 and 47 of the Constitution because it lacked public participation.

In the past week, trucks heading to Mombasa port were halted, creating queues stretching more than three kilometres. The disruption was compounded by scheduled upgrades to KRA’s Integrated Customs Management System (iCMS), which is central to import and export clearance.

System downtimeThe system went offline for more than three days. KRA said the planned 36-hour downtime from 6pm on Saturday, February 7, 2026, to 6am on Monday, February 9, was meant to improve performance and reliability. By Wednesday evening, however, the platform remained unstable.“We expected the system to be restored by Monday morning, but we could not transact, forcing KRA to reboot. Today, Tuesday, the system is working but slowly, as traders scramble to clear goods,” said clearing agent Roy Mwanthi.

KRA apologised for the disruption and urged cooperation. “KRA regrets any inconvenience caused and appreciates the cooperation of all stakeholders as we improve our service delivery,” the Authority said.

Even before the upgrade, Mombasa port was struggling with high container volumes and system bottlenecks. Authorities have announced measures, including transferring transit cargo to Naivasha ICD, moving containers that have stayed more than 21 days to Container Freight Stations and increasing use of the SGR to Nairobi and Naivasha to ease pressure. Officials describe the steps as short-term pain for longer-term efficiency gains.

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