Shipowners lobby objects new container cleaning charges at Mombasa port
Shipping & Logistics
By
Patrick Beja
| Nov 03, 2025
Shipowners want the controversial container cleaning charges restricted to agriculture imports and exports to mitigate the cost of doing business at the port of Mombasa.
Speaking through their lobby, Kenya Ships Agents Association (KSAA), the shipping lines argued that the charges were punitive.
In a letter to the industry regulator, Kenya Maritime Authority (KMA), the association said they would bear the Sh2,000 per vessel charges but oppose the Sh375 charged for cleaning a container at the port.
In March this year, Kenya Plant Inspectorate Service (Kephis) introduced the charges for cleaning a ship and a container at the port, leading to a standoff with the shipping lines.
In the letter addressed to KMA director general Omae Nyarandi, KSAA Chief Executive Officer Elijah Mbaru questioned the additional charges that became effective on November 1, 2025.
“As an industry, we want to play our part in resolving this issue, and we have stated that we will absorb the vessel inspection fees of Sh2,000 per vessel from inception. However, we not that this charge, wherever it rest, adds another cost to the country as a whole and as such we suggest that in order to mitigate that cost, the container charges be restricted purely to agricultural products, both import and export where there lies the greatest risk of contamination,” he said.
According to Mbaru, KSAA will be forced to charge such levies at the depot level to be absorbed by exporters and importers.
He urged KMA to restrict the container cleaning charges to only agricultural imports and exports to mitigate costs at the port, warning that the manner in which the container cleaning charges were being implemented might adversely affect port shipping business.
KSAA has rejected a proposal to charge them a fee for the container cleaning services at the port.
A meeting held at the KMA headquarters noted that shipping lines collect billions of shillings annually from shippers for container cleaning, repair, and handling fees, even though they do almost no actual work.
Kephis managing director Prof. Theophilus Mutui is now demanding transparency in the sector. Mutui is leading the campaign for container and vessel cleaning regulations at the port.
Shipping lines levy a cleaning fee of between Sh4,500 and Sh12,900 per container. With approximately 2.4 million containers projected to pass through Mombasa this year, the shipping line is expected to make billions of shillings.
In a meeting with KMA, players in the sector said that despite the exorbitant charges, only two per cent of containers were ever cleaned prior to Kephis entry in March this year.
"The irregular and unjustified fees are expected to be even more, with no transparent record of work done or accountability for the charges," said a source in the meeting.
The revelation emerged during a multi-agency stakeholders’ meeting at KMA offices, where industry representatives accused the shipping lines of exploiting traders.
Shipping lines were also accused of neglecting international cleanliness standards—a malpractice that has cost Kenya billions of shillings in lost export markets, jobs, and government revenue.
However, KSAA has dismissed the accusations, maintaining that all export containers are cleaned to ensure cargo is not contaminated with Mbaru assuring that all export containers are being cleaned to ensure the quality of cargo.
“What they are saying is a lie. The containers are cleaned 100 per cent because no one can go for a dirty container,” he stated.
Mbaru objected to the charging of shipping lines for container cleaning certificates because some of them charge cleaning fees to importers.
"We take note and applaud that the Kephis approach is a pioneer worldwide but strongly object to the way the onus to pay for a cleaning certificate is placed on shipping lines because some of them charge cleaning fees to importers," he told KMA in his letter.
Mbaru blamed the depot owners for making those claims in their pursuit of securing the container cleaning business at the port.