Why Kephis faces major hurdles in effecting ship, container inspection at port

A dispute has intensified at the port of Mombasa over the inspection of sea vessels and containers by the Kenya Plant Inspectorate Service (Kephis), which has reportedly caused delays to exports.

Shipping lines through the Kenya Ships Agents Association (KSAA) have also complained that charges levied for inspection are not transparent and justified.

KSAA chief executive officer Elijah Mbaru warned that any introduction of additional charges or procedural requirements should be carefully evaluated to avoid discouraging vessel calls or trade throughput or adding further cost to the logistics chain.

The ship's agents urged the government to ensure that Kephis inspections are restricted to plant-related cargo and not all types of goods passing through the port.

A vessel is charged Sh2000 per inspection, while a container is levied Sh375 and Sh2000 for its cleaning.

Kephis introduced the charges on March 1 this year, for inspection of ships and containers at Mombasa port and border points to prevent the spread of pests and diseases from foreign countries.

Managing director Theophilus Mutui had observed that the inspection ensured that vessels and sea containers are clean and do not bring materials that harbour pests and diseases from other countries.

But in a letter to Investment, Trade and Industry Cabinet Secretary Mr Lee Kinyanjui dated August 18, this year, KSAA said the charges levied in respect of inspection activities must be transparent and verifiable.

Meanwhile, Kenya Maritime Authority (KMA) has directed that no export container should be held back because of nonpayment of inspection of inspection related fees.

In a letter to Kephis managing director Prof Theophilus Mutui dated August 12, 2025, KMA director general Omae Nyarandi said pending arrears settlement will be discussed in an upcoming meeting.

Nyarandi also directed Kephis to furnish the authority with all relevant documentary evidence of adequate public participation being undertaken with regard to the implementation of the container vessel inspection.

The industry regulator also directed shipping lines not to introduce any inspection charge, as the same is already paid for as a container cleaning charge.

“Exports are critical to the Kenyan economy and government agencies are obliged to intervene and provide a way forward on any operational undertaking that is likely to hamper the seamless flow of the exports in the logistics chain,” he noted.

He said the current shutouts are attributed to the non-issuance of container inspection certificates to agricultural export containers owing to the non-payment of the respective inspection charges by the relevant shipping lines.

The shipping lines said such charges, where warranted, should be appropriately passed on to the responsible cargo interests, such as importers and exporters, adding that procures must be consistently aligned with international standards and regulatory frameworks, ensuring compliance with applicable trade laws and practices.

KSAA said that, where feasible, multiple compliant inspection options should be provided, allowing stakeholders flexibility in meeting regulatory obligations.

In the letter by Mr Mbaru, the shipping lines said the port operations must be fluid and unimpeded, ensuring that inspection activities should not disrupt access to storage, cargo handling or the broader logistics chain.

“In accordance with international norms, inspections should be ideally conducted at the port of origin, preferably at the shipper or consignee to minimise operational impact within the port,” he noted.

He said compliance requirements must be addressed at the earliest stage of the import/export process, before cargo is admitted into port facilities, to mitigate any operational interruptions.

He urged the government to ensure that the competitiveness of the port must be preserved; any introduction of additional charges or procedural requirements should be carefully evaluated to avoid discouraging vessel calls or trade throughput or adding further cost to the logistics chain.

“Further to our review and research, we have observed that the inspection regime under discussion should specifically target plant-related consignments and should not be broadly applied to all cargo types as currently proposed for implementation within the port of Mombasa,” he said.

Mbaru noted that such inspection practices are not conducted within port promises or storage facilities at other comparable international ports.

“These inspections should also be charged to the parties who would be importers and or exporters. We kindly emphasise the importance of maintaining the port’s competitive position in the region and trust that these considerations will guide forthcoming decisions. We would greatly appreciate your attention and intervention in this matter,” said the letter.