The Kenya Plant Health Inspectorate Service (KEPHIS) has defended its decision to introduce container and vessel inspection charges at the Port of Mombasa, despite a recent directive by the Kenya Maritime Authority (KMA) to suspend the fees due to concerns that they were slowing cargo movement.
Speaking in Mombasa, KEPHIS Board Chairman Joseph M’Eruaki said the inspections were critical to safeguarding the country from invasive pests and diseases, in line with international obligations under the International Plant Protection Convention (IPPC).
KMA had suspended the charges introduced to allow time for dialogue between government agencies and industry players.
The dispute stems from new fees introduced by KEPHIS in March 2025. Shipping lines were required to pay KSh 2,000 for vessels exceeding 10,000 tonnes, KSh 1,000 for smaller vessels, and KSh 375 per 20- or 40-foot container. With the Port of Mombasa handling about 1,750 vessels and over two million containers annually, the charges could have generated up to KSh 753 million annually for KEPHIS.
However, KSAA strongly opposed the levies, terming them a duplication of services already offered by other agencies such as port health, customs, immigration, and pollution control — all at no extra cost.
“KEPHIS lacks the technical and operational capacity to carry out these inspections and has provided no clear justification for charging fees on top of existing services,” said KSAA CEO Elijah Mbaru.
KMA Director General Omae Nyarandi backed the association’s position, warning that imposing new charges without harmonizing agency roles could create inefficiencies and increase costs for port users.
KEPHIS insists the fees are legal, citing the KEPHIS Act 2012, Plant Protection Act, Export Act, and Legal Notice 48 of 2009, alongside international standards.
Efforts to resolve the matter began in March when Mombasa County Government convened a meeting following KSAA’s petition. The parties agreed to develop a Memorandum of Understanding (MoU) to clarify roles and streamline inspections, but the agreement stalled.
As tensions escalated, KSAA formally petitioned Trade Cabinet Secretary Lee Kinyanjui in August, arguing the blanket application of the fees was “misaligned with global maritime practices.”
“Our review shows that inspections should be risk-based, targeting only plant and agricultural consignments,” Mbaru said. “Charging all cargo types undermines port efficiency and raises costs unnecessarily.”
KSAA also recommended exempting cargo with valid certificates of conformity from inspection to avoid duplication and delays.
“The sudden introduction of arbitrary charges creates uncertainty, raises the cost of doing business, and risks diverting trade flows away from Kenya,” Mbaru said.
This article was published by Githua Kihara, an editorial consultant for FEAFFA’s Freight Logistics Magazine. For any inquiries, please contact us via email at editorial@feaffa.com or freightlogistics@feaffa.com, or reach out to Andrew Onionga directly at onionga@feaffa.com or oningaam@gmail.com / +254733780240.
