Demurrage charges have seen ships pay up to $300,000 (Sh30 million) a month, which is now being passed on to consumers.
Wheat flour is increasingly an important substitute for scarce maize flour.
Farmers have been demanding higher prices for the local crop, which has forced millers to prefer imports.
Wheat flour prices have gone up for the second time since May with millers attributing the rise to delays in offloading grain at Mombasa port.
Demurrage charges have seen ships pay up to $300,000 (Sh30 million) a month, which is now being passed on to consumers.
Ship owners pay the charges for delayed loading or unloading. The retail price for a two-kilogramme packet is now Sh133 for Exe brand, up from Sh120 in May.
Golden is retailing at Sh129 up from Sh122 with Jimbi selling at Sh135. Most other brands are missing in some of the supermarkets.
“The prices will continue rising as long as it takes longer to offload the wheat from the ships,” said an official at the Cereal Millers Association who sought anonymity to avoid antagonising authorities.
Kenya Ports Authority managing director Catherine Mturi-Wairi had not responded to our inquiries by the time we went to press.
The delays, the millers say, have been occasioned by the priority given to white maize at the port.
Wheat flour is increasingly an important substitute for scarce maize flour.
The official said millers are currently relying on local wheat, which is more expensive than the imported one, making the cost of flour even higher.
Local wheat is selling at Sh3,200 a 90-kilogramme bag compared to the imported grain that goes for Sh2,600.
Farmers have been demanding higher prices for the local crop, which has forced millers to prefer imports.