Kenya’s port of Mombasa is straining under an endemic level of congestion, principally due to the weight of container traffic lingering in the port. Considered to be the most important seaport in East Africa, the Kenyan authorities have taken action to clear the backlog and get the port functioning more efficiently. The economic imperative is stark. Neighbouring countries send much of their overseas trade through the port, and that makes Mombasa vital to Kenya’s trade and economy overall.
A joint initiative by the government overseen corporations of the Kenya Ports Authority (KPA) and Kenya Revenue Authority (KRA) has seen measures introduced to ease congestion. The reforms are aimed at making the clearance of containerised traffic more efficient and predictable.
Empty-container handling changes
The KPA is seeking to deal with the problem of empty container movements slowing port operations. Historically, the port has allowed empties to be brought from depots directly to the vessel side. The KPA is now taking steps to limit the number of empty boxes processed at the port. These include a requirement that empty containers will now remain in intermediate storage depots for at least 72 hours before being moved to port. Shipping agents must submit requests for empty container handling at least seven days before vessel arrival, and empties must be delivered to the port no later than 24 hours before vessel arrival. The KPA is also taking steps to ration capacity, limiting call sizes to between 2,000 and 2,500 containers, except at Berth 20, local media report.
KPA Managing Director William Ruto said the changes follow discussions with key partners, including the Kenya Ships Agents Association (KSAA).
Stalling the flow of containers inbound should reduce the pressure to process sheer numbers daily. According to national news sources in Kenya, Mombasa’s traffic has been growing significantly. In 2024, the port handled just over two million TEU for the first time – an increase of more than twenty per cent on the previous year. That growth would appear to be the cause and effect of the current congestion crisis.
Pressure on supply chains
The KSAA says the congestion is linked to more than 20,000 empty containers at the port. They say that vessels are waiting at outer anchorage, unable to be processed. The KSAA has previously made calls for decongestion strategies and better hinterland connectivity.
Mombasa is served by Kenya’s Chinese-built “Standard Gauge Railway”, which should be a significant asset to help clear the backlog and improve throughput. As part of the solution, the principal inland container depots (ICDs) at Nairobi and Naivasha will now receive trains which will clear customs locally. That suggests that facilities will have to be established at those depots. Nevertheless, Nairobi ICD has the capacity to handle 450,000 TEU per annum (KPA figures), which could radically improve the situation 480km back down the tracks at Mombasa.
Pragmatic measures
Local reporting says that containers held at port for over 21 days (designated as ‘long stay’) are being moved to “customs licence peripheral facilities” and inbound intermodal cargo will be directed to “Container Freight Stations” for clearance, to free up yard capacity and improve flow. The Kenya Standard newspaper reported that other measures are to include 24-hour operation at the port, and the diversion of transhipment loads to the northern Kenyan port of Lamu.
However, shipping lines and industry groups have highlighted berthing delays, storage shortages, and slower truck turnaround times as factors still contributing to congestion. Dock workers are also reported as demanding clarity on bonuses and pointing to ongoing cargo congestion issues, warning that without further action, delays could worsen.
Association concerns
The Kenya International Freight and Warehousing Association says the problems at Mombasa may not be as readily solved as the agencies imagine. The Association says agents are facing challenges too, and that the measures to relieve the port may just be moving the problem back up the chain.
“We appreciate the fact that the anchor stakeholders have sat down and come up with extraordinary measures,” said Rajab Khamisi, the Association’s representative in Mombasa. “If implemented fully, we should see a port that is more fluid. Unfortunately, the shipping lines are yet to play ball,” he said.
Despite all this, Mombasa is still seen as a dependable port in the region. As reported by WorldCargo News, the port has been investing in greater handling capacity. However, demand continues to outstrip available effort. Reports from late 2025 indicated, for example, that ships were diverted from Dar-es-Salaam (Tanzania) due to congestion there. Mombasa remains under pressure.
