Offloading of subsidised maize at the Mombasa port has been delayed, raising fears of a shortage of the Sh90-a-packet flour in shops.
Millers have raised concern that they are not getting enough of the subsidised maize in what has reduced supply of the flour in the market.
Agriculture secretary Willy Bett said 1.4 million bags of maize are at the port waiting to be discharged, creating a shortage for the millers.
The delay at the Mombasa port signals a shortfall and rationing of the subsidised staple food.
Three ships carrying the last batch of 1.1 million bags of subsidised maize docked at Mombasa port before the October 26 repeat presidential and flour from the grain were expected to land in the shop shelves in the second week of November.
"The current shortage of supplies results from the fact that huge consignment of maize is stuck at the port waiting to be offloaded," said Mr Bett.
The maize cargo is equivalent to Kenya's consumption for 14 days.
Mr Bett said the market is yet to get enough stocks from the ongoing harvest in the North Rift due to rains, underling the importance of the 1.4 million bags of subsidised maize.
"We are not getting enough stocks currently at the National Cereals and Produce Board (NCPB) as we had anticipated as the purchases have been slowed down by rains," he said.
The NCPB had by Monday purchased 150,000 bags of maize out of 2.4 million bags that it targets to replenish the Strategic Food Reserve almost a month since it opened its silos.
The government has set aside Sh7.1 billion to buy a bag at Sh3,200 from the farmers.
The Treasury ended the maize import subsidy, which started on May 16, in mid-October.
The subsidy lowered the price of a 90-kg bag of maize to Sh2,300 from above Sh4,000 with taxpayers offering importers a rebate or the difference of about Sh1,700.
The end of the subsidy and the setting the NCPB price at Sh3,200 a bag is expected to raise flour prices to Sh120.
Millers will revert to the market price of maize once they exhaust the 1.4 million bags.
They expect to buy a bag at Sh3, 400 when transport costs are factored in, forcing them to increase flour prices by Sh30 from the current Sh90.
This looks to put pressure on inflation, which fell to a 16 month low of 5.72 per cent in October, pushed by a fall in some food prices.