Cargo congestion at the Port of Mombasa has reached critical levels, prompting traders and shipping industry players to call for drastic short-term measures to restore normal operations at the country’s main maritime gateway.
Importers and exporters now want all cargo clearance activities removed from the port for three months and relocated to Inland Container Depots and licensed Container Freight Stations.
They say the move would create much-needed space within the port and expedite the evacuation of cargo that has accumulated following a sharp rise in trade volumes.
The Port of Mombasa has recorded strong growth in both conventional and containerised cargo in recent years. In 2024, total cargo handled rose to 40.9 million metric tonnes, up from 35.9 million metric tonnes in 2023.
Container traffic has followed a similar trend, climbing by about seven per cent last year to more than two million Twenty-foot Equivalent Units (TEUs). The growth, however, has outpaced evacuation capacity, leading to congestion that intensified towards the end of last year and into early 2026.
Data from the Shippers Council of Eastern Africa (SCEA) shows that by December 31, between 50,000 and 52,000 TEUs were stacked within the port yards. The slow movement of cargo has also resulted in vessels queuing offshore, with at least 20 ships waiting as of January 4, 2026.
“These delays are a direct result of slow evacuation of cargo from the port,” SCEA chief executive Agayo Ogambi said. “We are now seeing ships waiting to berth while others anchor offshore because there is simply no space.”
Ogambi said the council is proposing a temporary suspension of clearance within the port starting January 15, 2026. “We are calling for a stop to all port clearance, including the within-five-days window, for three months to allow the port to decongest,” he said.
Under the proposal, all local cargo would be cleared at ICD Nairobi or designated Container Freight Stations, which would operate 24 hours a day, including weekends. Ogambi said the Kenya Ports Authority tariff should apply during the period to avoid additional costs for traders.
“This is about restoring fluidity at the port,” he said. “If we do not act now, congestion will worsen, vessel wait times will increase, and shippers will continue to suffer heavy losses.”
Industry players say congestion has been worsened by rail transport challenges, including delays in moving containers to inland depots and frequent equipment breakdowns. Faulty scanners at both the Port of Mombasa and the Nairobi Inland Container Depot have further slowed cargo processing.
“Railage has become a serious bottleneck,” Ogambi said. “The railing of containers to ICDs is no longer predictable, and this has caused major operational disruptions.”
Importers want Kenya Railways to increase the number of container trains and guarantee timely delivery to inland depots to support faster cargo evacuation.
The handling of empty containers has also emerged as a major pain point. Many empty depots in Mombasa are full, forcing trucks to queue for several days before offloading. Shipping lines have responded by imposing container demurrage charges, costs that traders say are eventually passed on to consumers.
Losses
The Kenya Ship Agents Association (KSAA) says congestion is costing shipping lines millions of shillings daily. “Delays in berthing translate to losses of between $20,000 and $50,000 per day, depending on the vessel,” KSAA said.
According to the association, some vessels have been forced to leave Mombasa without completing cargo operations due to berth pressure, resulting in lost capacity and disrupted shipping schedules.
Kenya Ports Authority managing director Captain William Ruto has acknowledged the storage shortage at the port. He said Mombasa was designed to hold about 8,000 TEUs but has been forced to accommodate far more due to the surge in volumes.
“We are dealing with a serious storage challenge,” Ruto said. “The port is holding containers well beyond its designed capacity, and that has affected operations.”
The situation has been worsened by the closure of the Mahati Container Freight Station, which reduced available storage space in Mombasa. Existing empty container depots, including Hakika, APM, Dodwell, Fortune, Cargo Haven and Port Reitz, are operating under pressure.
Global shipping disruptions have added to the strain. The Red Sea crisis forced vessels to reroute around the Cape of Good Hope, increasing calls at Mombasa as some shipping lines diverted cargo from other congested ports.
These challenges contributed to Mombasa’s drop in the World Bank’s 2024 Container Port Performance Index, where it was ranked 375th out of 403 ports worldwide, behind several regional competitors.
Shippers warn that unless urgent steps are taken to improve evacuation, storage and rail connectivity, congestion at the Port of Mombasa will persist, with far-reaching consequences for trade, shipping costs and consumer prices across the region.
It’s alarming to see Kenya’s busiest port in such severe congestion, with traders pushing for a drastic three-month clearance halt just to clear the backlog, this could disrupt regional trade and drive up costs for everyday goods if not resolved quickly.