A powerful business empire that has long controlled the port and cargo operations in Mombasa is now facing serious legal and administrative setbacks that are slowly breaking down its influence.
For more than ten years, Autoport Freight Terminals and Portside Freight Terminals, both companies with close ties to the family of Hassan Joho, the Cabinet Secretary for Mining, Blue Economy and Maritime Affairs, held major control over the transport of goods through Mombasa to countries like South Sudan.
Their grip on the logistics sector, especially in cargo handling and port infrastructure, remained mostly unchallenged. But this dominance is now being shaken by a mix of court decisions and policy changes.
Things started to shift in August 2023 when the Ministry of Transport and the Kenya Revenue Authority approved new players to take part in handling the more than 1.1 million tonnes of cargo that moves to South Sudan each year.
A letter from Transport Principal Secretary Mohamed Daghar made it clear that importers from South Sudan could now choose from any KRA-approved terminal. Companies like Compact Consolbase, Mombasa Container Terminal, and Mitchell Cotts were allowed to join Autoport in managing this business.
This marked the end of Autoport’s near-total control of that cargo flow. The change came after complaints from South Sudan and other cargo owners about delays, logistical challenges, and claims of unfair treatment and auctions.
Then in June 2025, the Supreme Court struck another blow by cancelling an earlier approval that had allowed Portside Freight Terminals to build a Sh6.4 billion bulk grain facility at the port.
The judges said the Kenya Ports Authority had wrongly used a special procurement method instead of an open tender process.
They stressed the importance of sticking to the Constitution and warned that even national security or food supply cannot be used as reasons to ignore fair procurement rules.
South Sudan, which is Mombasa’s second-largest customer after Uganda, also decided to change its cargo-sharing formula. It cancelled the old agreement that gave Autoport 80 percent of its cargo, saying the company caused delays and disrupted even UN consignments.
A new sharing model was introduced, giving Compact Freight 30 percent, Autoport 20 percent, and three other companies the remaining 50 percent. When the Kenya Ports Authority failed to follow this directive, Compact Freight went to court.
The High Court ruled that KPA must stick to the new formula, cutting Autoport’s share significantly while the case continues.
This ruling has hit Autoport’s income hard and reduced the Joho family’s power in the regional cargo business. Autoport responded by asking to join the court case as an interested party, arguing that it had invested heavily under the previous system.
The court agreed to this request and issued temporary orders to stop any cargo allocation that goes against South Sudan’s new directive until the case is heard fully.
Many see these court and policy decisions as part of a wider shift in how the port business in Kenya is run. The Joho family had built a strong network, including using the Standard Gauge Railway to move goods to Nairobi and proposing major port projects like an island grain berth.
But these advantages are now being challenged by legal requirements for openness and fairness.
Since President Ruto took power in 2022, his administration has pushed to open up key sectors that were once dominated by politically connected groups.
Even though Mr Joho later joined the Cabinet under a broader political deal, the companies linked to his family are still facing serious legal defeats.
With more court battles still ahead and only temporary protection from some orders, it is becoming clear that the Joho family’s long-standing influence over Kenya’s key trade routes is fading, one legal decision at a time.
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