National Development Implementation Committee (NDIC) has directed the National Cereals and Produce Board (NCPB) to halt further fertiliser distribution to farmers.
This follows a public outcry over the fertiliser's quality, sparking an ongoing investigation.
The NDIC, led by Prime Cabinet Secretary Musalia Mudavadi, met on Friday, March 29 and expressed concern.
"As a precautionary measure, the NCPB has been directed to suspend further distribution of fertiliser until the investigation is concluded and a report is provided," the committee said in a statement.
"The National Government reiterates its support for the farmers of our great nation to improve farm yields," the committee said in a statement.
The NDIC affirmed that those found guilty after investigations would face the law.
At the same time, Principal Secretaries were advised to ensure full compliance with procurement laws.
The meeting comes after contradicting directives on fertiliser sales were issued by Agriculture CS Mithika Linturi and Principal Secretary Dr Paul Ronoh.
In a tweet on his official page Thursday evening, the CS directed all National Cereals and Produce Board (NCPB) and Kenya Seeds Company outlets to remain open during the Easter holiday.
He said this is to ensure farmers are comfortable during the planting season.
"I have this evening directed NCPB & (sic) Kenya Seeds Limited outlets countrywide to remain open during the Easter holiday to facilitate our hard-working farmers needs in the ongoing planting season," Linturi tweeted at a minute past 9 pm.
A week before, the PS wrote to the NCPB Managing Director, Joseph Kimote, directing him to suspend the distribution of fertilisers to farmers.
Ronoh said the decision was reached after establishing that some of the fertiliser circulating had not met the required standards.
"Following a spot visit by Ministry staff led by the Principal Secretary to Counties and National Cereals and Produce Board stores, it was established that the above fertiliser being distributed under the subsidy programme may not be meeting the required standards as earlier indicated," the letter dated March 20 reads.
"Your institution is requested to suspend the distribution of this fertiliser with immediate effect from being issued to farmers."
The PS directed the NCPB to penalize suppliers whose fertilisers are below the required standard.
Speaking in Kuresoi, Nakuru County, days ago, Linturi dismissed claims of counterfeit state-issued subsidised fertiliser, saying that government fertilisers were scientifically tested and approved before circulation to Kenyan farmers.
"The fertiliser given to farmers by the government has been tested and we have all the analysis. The fertiliser is okay," Linturi said.