The cost of handling cargo at the port of Mombasa continues to increase with shipping lines paying up to Sh5 million per day over delays with lorries picking cargo at the port sometimes queuing for more than 24 hours.
At different depots around the port, there are long queues of lorries loaded with empty containers as the Kenya Transporters Association (KTA) estimates more than 600 lorries are still stuck due to lack of space to offload them.
This comes as allegations emerged of bribery for space in the container depots to allow some lorries to jump the queue.
"Shipping lines are making losses with about Sh5 million to Sh6 million per day for waiting to berth," said Kenya Ships Agents Association CEO Elijah Mbaru.
In the past week, there has been a long traffic stretch of more than 3 kilometres, made worse by the maintenance of the Kenya Revenue Authority (KRA) system.
Activities at the Mombasa port have not been running smoothly due to system disruption for scheduled maintenance of its Integrated Customs Management System (iCMS), a crucial platform for the clearance of both import and export cargo. It was taken offline for upgrades for more than three days, and has stalled cargo movement at the port of Mombasa.
The KRA system, which went offline on Friday for a planned 36-hour system maintenance, has resulted in long lorry traffic at the gateway.
The iCMS is a platform that supports customs operations, facilitating cargo clearance, revenue collection, and cross-border trade processes at ports of entry across the country.
Vehicles that were expected to pick up cargo from the port of Mombasa have been queuing, waiting for the system to be restored and consequently causing serious delays and losses to transporters.
In a statement, KRA had indicated that the disruption would last for 36 hours from Saturday, February 7, 2026, at 6pm to Monday, February 9, 2026, at 6am.
“We wish to inform partner government agencies, importers, exporters, clearing agents, shipping lines, and the general public of scheduled major maintenance for the iCMS," stated KRA.
The downtime has affected various users of the iCMS platform, including importers, exporters, clearing and forwarding agents, shipping lines, and some government agencies.
On Friday February 13, Roads and Transport Cabinet Secretary Davis Chirchir warned that government agencies that failed to comply with the set directives meant to reduce congestion at the port of Mombasa will be sacked.
“If I am here discussing operations, it means someone is not doing what is supposed to be delivered. There is a problem of coordination among government Partner agencies,” said the CS at the port of Mombasa.
In the past few months, different cargo handling agencies, Kenya Ports Authority, KRA and shippers have been shifting blame to each other on the increasing congestion.
Mr Chirchir authorised KPA to procure cargo handling facilities to speed up the handling process, which is short of more than 80 specialised tractors.
For short-term solutions, to decongest the port, the government has reintroduced mandatory rail haulage of cargo from Mombasa port to other landlocked countries.
The move has sparked protests among transporters, saying the directive was declared illegal by the High Court in 2020.
Since Friday last week, lorries picking cargo from the port have been suspended for a KRA system upgrade, which has not been fully reinstated a week later.
Due to that, lorries picking cargo from the port have caused a massive traffic gridlock forcing the KRA to direct all cargo destined to Uganda, South Sudan, Democratic Republic of Congo, and Rwanda be prioritised to be hauled to Naivasha Inland Container depot.
On Tuesday, KRA Commissioner General Humphrey Wattanga announced the prioritisation of Naivasha ICD for long-haul cargo bound for the neighboring countries due to increased cargo volumes at Mombasa Port.
Different port stakeholders, including clearing and forwarding agents and the KTA have strongly opposed any proposals to make the Naivasha ICD the mandatory route for cargo, saying such a move would be illegal, anti-market, and harmful to businesses and livelihoods along the Mombasa-Malaba corridor.
KTA Chairman Newton Wang’oo stated that the Naivasha ICD lacks commercial justification and that such a directive would infringe on a cargo owner's choice of clearance point and transport mode.
The KTA attributed port congestion to poor planning and vessel scheduling, not a lack of rail usage, and warned that forced rail haulage would violate constitutional provisions and court precedents.
KTA Chairman Newton Wang’oo described the directive as misguided, pointing out that the Naivasha ICD lacks defensible commercial or logistical justification and that no rational importer would voluntarily select it as a clearance point.
"The current congestion is a result of poor planning, vessel scheduling failures, and challenges in empty-container evacuation. Vessels are currently departing with sub-optimal load factors because they cannot wait to load empty containers. These failures will not be resolved through the forced diversion of transit cargo to Naivasha ICD,” said Mr Wang’oo.
In November 2020, the High Court revoked the directive by the Kenya Ports Authority (KPA) and KRA that all cargo from the Mombasa port to Nairobi be transported via the Standard Gauge Railway (SGR).
The five-judge bench consisting of Joel Ngugi, Lydia Achode, Pauline Nyamweya, Erick Ogola, and Anthony Mrima ruled that the directive violated articles 10 and 47 of the constitution as it did not go through public participation.
On March 15, 2019, and August 3, 2019, KPA issued a notice making it mandatory for importers to use the railway line to ferry containers to the Nairobi Inland Container Depot. The order sparked protests in Mombasa, with KTA moving to court challenging their constitutionality and legality, in court, where it argued it could lead to massive job losses in Mombasa.
