Anxiety as Mombasa port is slapped with surcharges amid ship delays

The recent spillover of ships from Tanzania following post-election violence and the traditional surge in cargo arrival every last three months of the year have combined to cause congestion at the port of Mombasa.

Kenya Ships Agents Association (KSAA) CEO Elijah Mbaru reported huge losses in ship charter fees after several ships had to wait to berth at the port.

This has forced Kenya Ports Authority (KPA) managing director William Ruto to ask shipping lines to direct ships carrying transhipment cargo to dock at the Lamu port, where there is adequate space.

At the same time, Kenya's largest shipping line, Maersk Line, is set to introduce an Operational Cost Import (OCI) fee at Mombasa port in reaction to the introduction of ship inspection and container cleaning charges by the Kenya Plant Inspectorate Service (Kephis) on March 1, 2025 to protect plants from foreign pests.

It is estimated that Maersk Line could collect upto US$8,027,602 (about Sh1 billion) annually from this surcharge alone and hence have a negative impact on competitiveness of the port and the economy.

In 2023, Maersk Line handled 292,259 container units at Mombasa port representing 30 percent of the port's throughput.

Meanwhile, the Mombasa port's problem has been worsened by delays in returning empty containers and the delay to deploy dedicated sweepers or specialised vessels to ship out the empties from Mombasa port.

It is estimated that 60 per cent of containers at the port are empties waiting to be shipped out to ports that need them like those in China where manufacturing is booming.

Last week, shipping lines revealed the full implications of ships and a pile-up of empty containers at the Mombasa and Dar es Salaam ports on the shipping industry.

KSAA disclosed that shipping lines have been grappling with poor and slow operation at the Mombasa and Dar es Salaam ports, including delays in ships berthing that have caused heavy losses in terms daily charter/demurrage fees.

According to Mbaru, the losses are estimated to be US$20000 (Sh2.6 million) to US$50000 (ShSh6.5 million) daily per ship, depending on vessel size.

About 20 ships wait to berth daily following an acute congestion, even as more ships are scheduled to call at the port.

Several ships re-routed to Mombasa from the port of Dar es Salaam after it was shut down during the elections.

Maersk Line will introduce the OCI fees by December 1, 2025 for shipments destined to Mombasa port.

A 20 foot container of dry cargo will attract US$18 (Sh2,322), 20 foot of reefer container US$33 (Sh4,257) and a 40 foot container of reefer container US$43 9Sh5,547).

"This surcharge is being implemented to offset the additional operational expenses associated with container inspections. The OCI fee will be invoiced alongside the freight charges," said the shipping line in a notice dated October 31, 2025.

This was in reaction to the introduction of Sh375 for cleaning of a container and Sh2000 for inspection of a ship at the port by the Kephis.

Shippers Council of East Africa (SCEA), CEO Agayo Ogambi, called for an engagement with the Maersk and the industry regulator, Kenya Maritime Authority (KMA) on the OCI surcharge, warning that it will negatively impact on the port business and the economy.

"Our members have expressed deep concern regarding the potential implications of this cost on the competitiveness of Kenyan imports, the overall cost of doing business and the stability of supply chain operations," Ogambi said.

Mbaru noted that the lines face an acute shortage of empty containers in key ports such as China which are leading sources of manufactured goods.

“Lines are experiencing an acute shortage of empties in deficit location like the major Chinese ports, China being world's number one manufacturer and exporter equal there is a massive shortage of empties in the world busy trade routes like the Asia-Europe, Asia-USA” he explained.

In a statement, the lines have not been able to load full tonnage of ships leaving Mombasa as in some instances they are made to vacate berth without completing cargo operations.

“There is need for (Mombasa) Port to create handling and storage facility inside the port area instead of relying on the depots; despite being independent entity, they are not creating alternatives for influx and overflow,” Mbaru argued.

He said it was critical that the steel boxes are part of the ship and if commercial fluidity is to be realised on the containers just like the ship should always be in motion.

“Our rallying cry as ocean carriers is for consignees to return empties at the earliest possible time and the port to load maximum empties as per bookings always provided,” he said.

Speaking during the annual general meeting at Tamarind Hotel in Mombasa last week, KSAA officials raised fresh concerns over the persistent congestion and rising operational costs at the Port of Mombasa, warning that inefficiencies threatened the competitiveness of the country’s biggest seaport.

The officials complained that the congestion has forced ships to wait to dock and hence caused them huge losses in waiting charges.

KPA and Kenya Revenue Authority (KRA) have come up with measures to clear the port of containers, including moving them to Naivasha and Nairobi Inland Container Deports (ICDs), private Container Freight Stations (CFSs) in Mombasa and encouraging transshipment cargo to be landed at the Lamu port.

KSAA chairman Roger Dainty, said congestion has persisted throughout the year after it carried over from the surge in ship arrivals typically experienced in the last quarter of 2023.

He noted that the congestion has slowed port productivity, constrained the evacuation of empty containers and caused a build-up in container depots.