Businessman Samuel Kairu Njonde, the man behind Compact Freight Systems, has emerged as one of the prominent names linked to an explosive investigation into an alleged Sh500 million customs fraud scheme at the Port of Mombasa.

The investigation, being jointly conducted by the Directorate of Criminal Investigations (DCI) and the Kenya Revenue Authority (KRA), has already led to the arrest of eight government officials and is now widening to include freight forwarding firms and businessmen suspected of facilitating the irregular release of cargo containers without payment of mandatory customs taxes.

How the Alleged Sh500 Million Port Fraud Worked

According to investigators, the alleged customs fraud scheme relied on the recycling of legitimate customs entry numbers that had already been processed and approved.

Rather than generating fake documentation, suspects allegedly reused previously cleared customs records and attached them to fresh consignments, allowing containers to exit the Port of Mombasa while appearing fully compliant with customs procedures.

Authorities believe at least 238 containers may have been irregularly cleared between 2025 and early 2026, although investigators fear the final figure could exceed 300 containers.

The suspected tax losses are estimated at more than Sh500 million.

Eight Officials Arrested in Mombasa Port Probe

Investigators say the operation involved a sophisticated network spanning both public and private sectors.

Already, five Kenya Revenue Authority officers and three Kenya Ports Authority employees have been identified as key suspects in the ongoing probe.

Authorities further allege that retired Kenya Ports Authority employees’ login credentials were unlawfully used to access port systems and process container releases under dormant digital identities, making the fraud difficult to detect.

The scandal has once again exposed deep vulnerabilities within Kenya’s most important maritime gateway.

Samuel Kairu Njonde and Compact Freight Systems Under Scrutiny

While no criminal charges against Samuel Kairu Njonde have been publicly announced, investigators are reportedly examining the role of freight forwarding companies linked to suspicious cargo movements through the port.

His company, Compact Freight Systems, has repeatedly surfaced in reports surrounding the ongoing inquiry.

The businessman’s name has long featured in legal and commercial disputes tied to cargo handling and logistics operations.

Previous Court Battles Involving Compact Freight Systems

Court records show Compact Freight Systems has previously been involved in multiple legal disputes concerning cargo handling, contractual disagreements, and claims of lost consignments.

One of the most notable cases involved allegations surrounding the disappearance of 153 bales of imported garments valued at more than USD 214,000 at the company’s Miritini-based container freight station.

Several court proceedings between 2022 and 2024 focused on liability for missing or damaged cargo.

The company has also faced creditor disputes.

In one long-running matter involving Aswan Developers and Contractors Limited, judgment was entered against Compact Freight Systems for approximately Sh6.8 million.

Attempts to stop execution of the decree reportedly failed, prompting auctioneers to target company assets, including a Reachstacker machine critical to cargo-loading operations.

South Sudan Cargo Dispute

Kairu’s company was additionally linked to a high-profile dispute involving cargo transportation arrangements for South Sudan.

The disagreement reportedly involved entities associated with former Mombasa Governor and Cabinet Secretary Hassan Joho and escalated into diplomatic and legal corridors after South Sudan terminated certain cargo allocation arrangements.

Justice Martha Mutuku later directed the Kenyan government to comply with requests arising from the cancellation of transport agreements involving Compact Freight Systems and Autoport Freight Terminal.

Port of Mombasa Corruption Concerns Resurface

The latest probe has once again placed the spotlight on corruption and tax leakages at the Port of Mombasa, a strategic trade hub serving Kenya, Uganda, Rwanda, South Sudan, and the Democratic Republic of Congo.

Over the years, the port has been hit by multiple scandals involving:

• Container diversion
• Tax evasion
• Cargo theft
• Under-declaration of imports
• Manipulation of customs systems

Anti-corruption agencies have repeatedly warned that criminal cartels operating within the maritime sector often rely on insider access within government agencies to bypass controls and facilitate illegal cargo movement.

Investigators Trace Containers and Money Trails

Authorities say the current fraud scheme did not rely on crude document forgery but instead exploited weaknesses within electronic customs systems and internal controls.

This allegedly allowed the operation to continue for months before investigators uncovered irregularities.

As DCI and KRA officers continue tracing the movement of hundreds of containers and following financial trails linked to freight forwarding firms, pressure is mounting on authorities to determine whether the scandal was the work of a few rogue officials or evidence of a much larger cartel embedded within Kenya’s maritime logistics sector.

For Samuel Kairu Njonde, whose business empire has remained deeply involved in East Africa’s cargo movement industry for years, the ongoing investigation now represents the most serious scrutiny yet.

Whether investigators ultimately establish direct criminal culpability or merely business association remains a matter for the ongoing inquiry.

What is already clear, however, is that the unfolding scandal has once again exposed the enormous financial risks posed by corruption and systemic weaknesses at one of Africa’s busiest ports.

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