Port users decry increased levies by state agencies

A cargo ship wait for offloading at Mombasa Port. April 17,2025. [Omondi Onyango, Standard]

Port stakeholders have raised concerns over increases new levies by government agencies at the port of Mombasa.

While some of the port users agree that some of the services rendered by state agencies are important, others have raised their opposition over the fragmented manner and possible delays in the clearance of cargo.

In the latest move, the government now wants all cargo entering and exiting Kenyan ports of entry to undergo specialised screening to detect and prevent illicit trafficking of special nuclear and other radioactive materials.

The decision by the Kenya Nuclear Regulatory Authority (KNRA) has caused concerns that it will delay operations at the port of Mombasa, which is currently facing congestion and delays, and also lead to increased costs of doing business.

In a recent notice to importers, exporters, and licensed cargo agents, KNRA said containerised cargo must pass through monitors stationed at strategic points, such as Mombasa port and Inland Container Depots (ICDs).

“These monitors provide non-intrusive, highly sensitive detection of gamma and neutron radiation. All legitimate radioactive sources must be accompanied by a valid KNRA import license. Accurate documentation, including the correct harmonised system codes, is required,” said KNRA in the notice.

The implementation start date was first set for May 1 this year, but was later deferred to July 2026 to allow more consultation. Stakeholders have already complained of the Sh1000 charge for screening a container.

The authority that regulates the safe, secure, and peaceful utilisation of atomic energy and nuclear technology, and the production and use of radiation sources and radioactive waste management, is headed by Director General Mr James Chumba.

“Importers and agents must ensure truck drivers and terminal operators follow designated traffic flows to avoid bypassing security checkpoints,” said KNRA, urging cooperation with the authority and multi-agency teams to minimise clearance delays.

In March last year, port stakeholders, including the Shippers Council of Eastern Africa (SCEA) and Kenya Ships Agents Association (KSAA) protested when Kenya Plant Health Inspectorate Service (Kephis) introduced Sh2,000 for vessel inspection and Sh375 per container cleaning at the port to control pests and diseases.

KSAA chief executive officer Mr Elijah Mbaru has been particularly opposed to the introduction of Kephis ship and container levies and their impact on port operations.

But Kephis managing director Prof Theophilus Mutui had explained that the move was aimed at reducing pest importation, although the fees faced opposition from logistics stakeholders who complained of additional costs of doing business at the port.

This week, SCEA chief executive officer Mr Agayo Ogambi said they were concerned about possible delays caused by the screening for nuclear and the increased costs through the fee.

“We appreciate the importance of securing the country from possible effects of nuclear and radioactive materials not authorised or approved, but are very concerned about possible delays in cargo clearance time and increased costs,” he said. 

He argued that the port throughput has increased exponentially, and there are resultant delays, congestion against limited capacity, and shippers have to wait longer for their consignments.  

He proposed that the government introduce appropriate funding mechanisms for government agencies, facilitating trade at the port. 

Ogambi suggested the setup of a single fund where agencies offering additional safety and control measures can draw funds for their operations instead of the fragmented levies. 

“We urge the government to engage the private sector to explore appropriate funding mechanisms for government agencies facilitating trade. Establishing a pool government service fee of say Sh3000 per container to support the National Environment Management Authority (NEMA), KEPHIS, Agriculture and Food Authority (AFA), Kenya Bureau of Standards (KEBS), KNRA, and all other agencies, for example, could be considered,” he noted. 

Ogambi noted that the agencies could draw their money for services provided from the fund instead of introducing individual levies at the port. 

He noted that with the Kenya Ports Authority (KPA) free period limited to five days, any delays are catastrophic and costly. 

“We hope to engage the nuclear authority to appreciate the standard operating procedures to be deployed, capacity, and if there are any exemptions, how payments shall be made,” he stated. 

He noted that ff the KNRA order affects cargo from transit countries, then further engagements with the landlocked countries should take place. 

“Unfortunately, if the other regional ports become more competitive than us, then we may lose the regional market currently at 30 percent of the total port throughput,” he said. 

SCEA wants exports to be exempted from the screening requirement unless the importing countries make it mandatory. 

Ogambi noted that agencies could draw their money for services provided from the fund. “It is not lost that businesses pay Import Declaration Fee (IDF) and corporate tax, which could meet the costs. 

“Since we appreciate that there may not be adequate funding, having each agency levy is costly and hurts businesses,” he noted. 

He argued that protecting the country from the port of loading would be more effective, and the nuclear authority could also consider a risk-based inspection.