Shipping industry players are grappling with financial losses amid rising operational costs and delayed shipments due to congestion crisis at the Mombasa port.
A spot check showed that some shipping lines were paying more than Sh5 million daily for unattended vessels, even as an average of 500 empty containers remained on trucks waiting to be offloaded due to limited space at the six available empty container depots.
The Mombasa port has recorded persistent delays since October last year, with about 20 vessels waiting at any given time as a blame game continues over responsibility for the inefficiencies.
The increasing cost of cargo delivery at the port has shifted vessel patterns, with shippers now preferring to call at Dar es Salaam instead of Kenya.
Previously, most vessels docked at the Port of Mombasa before proceeding to Tanzania, but delays occasioned by poor cargo flow at the port have changed this pattern.
The Kenya Ships Agents Association (KSAA) says it costs an average of Sh4.4 million to hire a vessel per day, excluding other running expenses such as fuel, insurance, and maintenance. This means that the current disruption in cargo movement continues to drive up freight costs across the region.
‘Port congestion at the Port of Mombasa continues to place heavy operational and financial pressure on shipping lines. When vessels remain idle for extended periods, costs escalate rapidly, with crew costs also rising as delays extend working time and welfare obligations,’ said KSAA chief executive Elijah Mbaru.
The Mombasa port has been receiving increased cargo volumes, but yards, empty container depots, handling terminals, and scanners remain inadequate.
At the Port Reitz cargo exit station, the rail-mounted cargo scanner has been out of service for about two months, causing significant delays in processing cargo for the standard gauge railway by the Kenya Railways and the Kenya Revenue Authority (KRA).
Due to the breakdown, containers must now be scanned upon arrival at the Nairobi Inland Container Depot, where only two out of four drive-through scanners are operational, resulting in severe congestion and delays.
‘We are working on it to ensure the scanners that have issues are repaired very soon,’ said KRC managing director Philip Mainga. The Kenya Ports Authority and the KRA have taken measures to decongest the port, but with little success.
In November last year, the duo directed importers with long-stay containerised cargo to clear local cargo at container freight stations in Mombasa, while transit cargo was to be cleared at either Nairobi or Naivasha but the directive was never implemented.
All long-stay containerised cargo at the port was to be transferred to customs-licensed peripheral facilities, while cargo destined for Mombasa was to be moved to container freight stations for final clearance. Cargo destined for Nairobi and other upcountry destinations was to be railed to the Nairobi ICD for clearance.
To free up more space, KRA was to conduct scrutiny to identify cargo eligible for auction, while approved cargo for destruction was to be transferred to licensed destruction sites.
KRA was also expected to immediately geofence Gate 24 to allow the exit of transit cargo and all consignments fitted with regional electronic cargo tracking seals, in addition to Gates 18 and 20 already in use.
Further, all cargo stakeholders were expected to harmonise working hours and shift management to ensure seamless processing of consignments, but this was never implemented.
KPA last week 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 said that all empty containers will 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.
Traditionally, logistics teams are allowed directly load empty cargo containers onto ships from storage depots to the terminal crane area for immediate loading, circumventing the lengthy process of intermediate storage at the port.
‘Following several engagements with key stakeholders, including Kenya Ships Agents Association (KSAA) and its members, the KPA has issued measures with effect from January 26, 2026, where all shipping lines representatives and their appointed agents are expected to strictly comply to reduce current congestion,’ KPA Managing Director, William Ruto, said.
‘Among the measures include suspension of handling of any empty container without advance clearance and submission at least seven days prior to the arrival of the vessel,’ he added.
The KPA boss said that empty containers will not be allowed into the port 24 hours before vessels berthed for collection.
‘Vessel agents/line representatives shall submit projected empty container loading requirements at least seven days prior to vessel arrival. The authority shall allocate empty container space per berth, capped at 2,000-2,500 containers except Berth No. 20. Any request to exceed this allocation must receive written approval from the Head of Container Terminal at least 72 hours before vessel arrival or planned berthing,’ Mr Ruto said.