The Kenya Bureau of Standards (Kebs) and millers have raised concerns over high levels of aflatoxin in maize.
They say most of the maize contains unacceptable levels of the toxin, making it unfit for human consumption.
Poor storage facilities and heavy rains in maize-growing zones have contributed to the problem, said Dr Henry Rotich, the director of meteorology and testing at Kebs.
"Regular inspections and tests for aflatoxin are carried out to ensure maize flour and other products meet recommended standards," he said.
"In Kenya, the allowable aflatoxin level in maize is 10 parts per billion. Anything above that is unacceptable."
Millers are also lamenting the aflatoxin contamination. The Grain Belt Millers Association (GBMA) Wednesday said the contamination has worsened the already acute shortage of maize -- from last season's 44 million bags to 33 million bags.
"We are currently operating at 30 per cent production capacity due to low supply of maize caused by challenges of high aflatoxin content," GBMA chairman Kipng'etich Mutai said.
The association brings together more than 35 small-scale millers, who have petitioned the government to review the acceptable aflatoxin level from 10 to 20 parts per billion.
"Most of the milling firms risk closure after Kebs introduced stringent measures to check aflatoxin contamination," Mr Mutai said.
He disclosed that maize from western Kenya and the lower eastern parts of Meru and Ukambani have high levels of aflatoxin.
Uasin Gishu and parts of Trans Nzoia have acceptable levels of the toxin, he added.
"Although there is some maize in the market, we cannot mill it because it has high aflatoxin levels. In most cases, they end up in informal market posho mills and finally finds its way to households for consumption."
He said millers have invested more than Sh1 million to procure machinery for testing aflatoxin as part of conditions introduced by the standards agency to guarantee the quality of maize flour.
Aflatoxin is produced by a fungus that grows on certain crops, such as maize and groundnuts.
Kebs suspended 17 maize flour brands late last year for containing high levels of aflatoxin.
Dr Eliud Kiplimo Kireger, the director-general of the Kenya Agricultural and Livestock Research Organization, said Kenya's food problems are compounded by "aflatoxin is in the soil".
"It is all over the country. We have not understood why it is high in some areas," Dr Kireger said.
Dr Sam Kibet Chebon, a researcher at Jomo Kenyatta University of Agriculture and Technology, said using uncertified seeds, premature harvest of the maize crop, especially during the rainy season, and continuous cultivation of the same crop on the same parcel of land contributes to a high incidence of aflatoxin contamination.