A section of Mombasa Port terminal 2. The terminal is used to reduce congestion of containers at the Port. 4th April 2023.[FILE,Standard]
KPA to roll out 24-hour schedule in fresh port decongestion bid
Shipping & Logistics
By
Patrick Beja
| Nov 12, 2025
The Kenya Ports Authority (KPA) and Kenya Revenue Authority (KRA) have inked a deal to speed up the processing of cargo at the port of Mombasa amid rising volumes.
On Wednesday, KPA’s ship list indicated that at least 50 ships were lined up to dock at the port as the import business enters the high season ahead of the festive season.
The new measures are also intended to free up space at key facilities serving Uganda, South Sudan, the Democratic Republic of Congo, Burundi, and northern Tanzania.
Port stakeholders, such as Nassib Mbarak, however, termed the deal a knee-jerk reaction to the impending congestion at East and Central Africa’s biggest port.
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Mbakak said KPA should have adequate cargo handling equipment and a robust clearance system to ensure faster clearance of goods.
“It is necessary to come up with extraordinary measures to free up space and ensure the port is not congested. There is a need for faster clearance of cargo to ensure the port is efficient, and hence the measures are welcome,” he stated. Mbarak said there is also a need to streamline the management of empty containers, which have been congesting the port, and ensure they are removed from the port as soon as they arrive.
He argued that transhipment cargo, which has been redirected to the more spacious Lamu port in the new measures, should also be removed faster to ensure the regional economies are well serviced by the two international ports.
“If these measures are implemented and the port cargo clearance system downtime challenge is addressed, the congestion problem will have been resolved,” he argued.
Mbakak said importers and exporters should be sensitised on the need to embrace pre-arrival clearance of cargo to ensure the port is fluid.
Container Freight Stations (CFSs) Association Chief Executive Daniel Nzeki welcomed the new port decongestion measures, saying they would go a long way in easing pressure on the facility.
“The port is essentially a transit facility meant for loading and unloading cargo and not for cargo storage. If we use the port as a storage facility, it will be congested. The new measures at the port are a step in the right direction. They will improve efficiency at the port,” Nzeki stated. He observed that the CFSs are currently 54 per cent full, projecting that cargo volumes would grow.
In the communique signed at KPA headquarters in Mombasa, KPA and KRA agreed that the port will operate for 24 hours, and long-stay cargo will be auctioned to reduce congestion.
The measures followed a meeting chaired by the executive office of the president’s council of economic advisors, led by former National Treasury Cabinet Secretary Henry Rotich and attended by several port stakeholders, which discussed measures to make the port efficient amid growth in cargo volumes.
“To facilitate 24/7 operations at the port, all cargo interveners shall harmonise their working hours and management of shifts to ensure seamless processing of cargo consignments,” said the two agencies.
The agreement, prepared by KPA Managing Director Captain William Ruto and KRA’s Commissioner of Customs and Border Control Dr Lilian Nyawanda, said all long-stay containerised cargo at the port will be transferred to the customs-licensed peripheral facilities.
It stated that containerised cargo destined for Mombasa will be transferred to CFSs for final clearance, containerised cargo destined for Nairobi and other upcountry destinations will be railed to the Nairobi Inland Container Depot (ICD), while containerised cargo destined for Uganda will be transferred to the Naivasha ICD for clearance.
In a bid to encourage the evacuation of containerised cargo, KPA and KRA agreed to waive 100 per cent of accrued storage and warehouse rent for long-stay cargo on lodgement of a waiver application by the affected customers for a period of 30 days.
“Considering the prevailing circumstances, the shipping lines are directed to waive container detection and accrued demurrage charges for the exercise to be successful. All primary port charges, rail freight charges, shipping line fees, and statutory taxes remain payable,” said the communique aimed to address growing congestion at the port.
The two agencies agreed that KRA will determine all cargo qualifying for auction and sustain gazettement of the consignments for importers to clear, failure to which the cargo shall be auctioned.
They said approved cargo for destruction will be transferred to licensed cargo destruction sites.
In the new measures, all vessels with transhipment cargo were encouraged to call at the port of Lamu to take advantage of the higher capacity.
Captain Ruto said that a ship with transhipment was diverted from Dar es Salaam to Lamu port following the recent conflict over elections in that country.
“All vessels with transhipment cargo are encouraged to call at the port of Lamu to take advantage of the higher capacity. To promote this, KRA will facilitate the use of supplementary manifests at no extra charge,” says the agreement.
In an effort to reduce truck turnaround time, all CFS-bound containers, once scanned, will be transferred to their respective CFSs, and the cargo image analysis and iScan message will be sent thereafter. It was agreed that KRA will carry out risk-based scanning for transit cargo.
To improve traffic fluidity at the port, Kenya Railway Corporation (KR) will provide shunting schedules, while port police, KPA and KR will put measures in place that ensure that the intersections are free of any obstructions from either trucks or rail wagons.
KRA will also immediately geofence Gate 24 to exit the port in addition to other gates already in use, such as Gates 18 and 20.
KPA and KRA said all domestic containerised cargo for port clearance that was not cleared within the allowed storage-free period of five days will be moved to CFSs.
“Importers are encouraged to nominate a CFS of their choice; failure to which KPA will nominate the consignments to any of the CFSs in the vicinity of the port,” said the agreement.
It was agreed that all container interventions by Participating Government Agencies (PGAs) will be undertaken outside the port in alignment with the government directive on multiagency interventions, where all the issues are resolved within five days.
KRA was tasked to implement the Pre-Arrival Processing (PAP) of cargo.
“In the medium term, the government has put in place measures to align all policy actions and system digitisation initiatives to provide long-term port efficiency to ensure the port of Mombasa remains the region’s preferred port of choice,” they said.
Separately, KPA and the Kenya Pipeline Company (KPC) also signed a strategic cooperation agreement aimed at boosting operational efficiency and safety at the Port of Mombasa oil terminals.
The partnership was described as a significant milestone in inter-agency collaboration through rehabilitation of the firefighting system at Pump Station No. 14 at the new Kipevu Oil Terminal.
The deal was signed by Captain Ruto and his counterpart Joe Sang to demonstrate commitment to strengthening critical infrastructure for Kenya’s petroleum logistics and energy security.
The collaboration was also aligned with the expansion of key port facilities facilitated by the new terminal, including the connection of Berths 14 and 16.
Ruto described the partnership as a major step forward for national infrastructure and safety systems.