Reprieve for cargo owners as agency halts vessel inspection levies

The maritime regulator has temporarily stopped container and vessel inspection charges introduced by the Kenya Plant Health Inspectorate Service (Kephis) at the Mombasa port.

The decision by the Kenya Airports Authority (KMA) is intended to allow government agencies and industry stakeholders to address the increasing disputes surrounding the contentious levies.

KMA states that the fees were initially introduced via Legal Notice No. 48 of 2009. However, changing market conditions and regulatory environments have complicated their implementation.

Meanwhile, a consultative meeting between Kenya Ports Authority (KPA), Kephis, and the Kenya Ships Agents Association (KSAA) has been convened for later this week to chart a way forward. 

The levies were designed to facilitate compliance with the International Plant Protection Convention (IPPC) standards, which mandate the inspection of all ships and freight containers to ensure they are free from pests and contamination when entering or leaving the country.

In March this year, Kephis rolled out new inspection charges. Under the new framework, shipping lines were to pay Sh2,000 for vessels exceeding 10,000 tonnes, Sh1,000 for smaller vessels, and Sh375 for both 20-foot and 40-foot containers.

The measures were implemented on a pilot basis, beginning 1 March 2025, following what Kephis termed “extensive consultations” with industry players.

Given Mombasa handles approximately 1,750 vessels and over two million containers annually, Kephis would have generated an estimated Sh753 million in additional revenue each year.

KSAA expressed strong opposition to the new levies, alleging that Kephis was duplicating services already offered by other competent government agencies free of charge.

KSAA Chief Executive Elijah Mbaru said port health, immigration, port state control, International Ship and Port Facility Security (ISPS) Code officers, pollution control officers, and customs officials already conduct inspections without levying fees on vessels.

“Kephis lacks the technical and operational capacity to undertake the inspections it is charging for and has failed to demonstrate any justification for the duplication of services,” said Mbaru.

KMA Director General Omae Nyarandi backed KSAA’s position, stating that imposing new fees without clearly defined roles and coordination among government agencies risked creating inefficiencies and unnecessary costs for port users. In an earlier interview, Kephis defended its position, insisting that the new levies were grounded in law.

The agency cited the Kephis Act of 2012, the Plant Protection Act (Cap 324), the Export Act (Cap 319), Legal Notice 48 of 2009, and international IPPC standards as the legal framework underpinning the charges.

“Kephis is committed to enforcing inspection measures as communicated with stakeholders and as mandated by both domestic and international legal instruments,” the agency stated in March.

The controversy drew the intervention of the Mombasa County Government, following a petition by KSAA.

According to Dr Noah Akala, the chief of staff, the county convened a consultative meeting on March 14, 2015, at the Council of Governors’ offices.

The meeting resolved that the county government would sign a Memorandum of Understanding (MoU) with Kephis to establish a structured approach to container and vessel inspections.

The MoU was expected to streamline processes and define the respective mandates of the agencies involved.

However, the agreement was never finalised, and Kephis proceeded to implement the charges until KSAA escalated the matter to KMA, the statutory regulator of the maritime sector.

Stakeholders in a meeting on 25 decided that the inspection regime should specifically target plant-related consignments rather than being broadly applied to all cargo types.

On August 18, KSAA wrote to the Cabinet Secretary for Trade, Investment, and Industry Lee Kinyanjui, saying the fees did not match international shipping standards.

It pointed out that Kephis had moved from the port area, making it harder to carry out inspections effectively.

“Our review indicates that the inspection regime should be risk-based, focusing only on plant and agricultural consignments. The blanket application across all cargo categories is unjustified and could undermine port efficiency,” Mbaru said. KSAA has recommended that government agencies boarding vessels should not impose additional charges.

The lobby further urged that cargo accompanied by certificates of conformity from the port of origin should be exempted from further inspections to avoid duplication and delays.

Mbaru reiterated that policy interventions at the Mombasa port should prioritise efficiency and competitiveness.

“The sudden introduction of arbitrary charges creates uncertainty for investors, increases the cost of doing business, and risks diverting trade flows to alternative routes,” he warned.

The suspension of Kephis charges comes at a time when the KPA has already carried out a review intended for a broader tariff adjustment that could see port charges increase up to fivefold across Mombasa, Lamu, and inland container depots.

The review, guided by Maritime Business and Economic Consultants, a firm led by former KPA executives that secured a Sh14.8 million consultancy contract, proposes hikes in vessel fees, cargo handling charges, storage penalties, and port access costs. The review has already received stakeholders’ inputs.

KPA has defended the proposed increases, citing rising costs of fuel, labour, equipment maintenance, and inflation. The authority said its current tariffs are lower than those charged at competing ports such as Dar es Salaam and Djibouti.

However, the Federation of East African Freight Forwarders Associations (FEAFFA), the Shippers Council of Eastern Africa (SCEA), and KSAA have strongly opposed the proposal.

They warn that the hikes could increase logistics costs by up to 27 per cent, erode the competitiveness of the Port of Mombasa, and divert shipping traffic to rival regional ports.

Critics further argue that despite charging in US dollars and benefiting from favourable exchange rate movements, KPA has not significantly improved operational efficiency. Labour shortages, congestion, and vessel delays continue to plague the port.

The business community has cautioned that both the Kephis levies and the proposed KPA tariff hikes would eventually be passed on to importers, exporters, and consumers, raising the cost of doing business and inflating consumer prices across the region.