Agriculture Cabinet Secretary Mithika Linturi now says only 3,000 bags of fertiliser in the market were found to be substandard.
The CS said the government's e-voucher system is foolproof enough to easily trace when the bags were supplied.
The system, Linturi said, has the capacity to tell who were the beneficiary farmers who picked the bags from the government stores.
"Only 3,000 bags were involved in this; We have an e-voucher system that we use and anybody who picks fertiliser we would trace you to the time and the store that you picked,'' he said.
Speaking in an interview on Citizen TV on Thursday night, Linturi said that the fertiliser that was being supplied under the government subsidy programme was of quality standard.
"The problem arose with a certain batch and this batch is known, where the fertiliser has been supplied to is known and we have told the affected farmers to return that fertiliser,'' Linturi said.
When pressed if the figures he had given were accurate, Linturi said the 3,000 bags were the ones that had been validated and confirmed as having been substandard.
"The Deputy President is my boss and can speak for himself; I am telling you about the figures that I am sure of and the ones I have been able to verify from my end,'' Linturi said.
The CS said he would stick to facts that have been validated when addressing the issues of substandard fertiliser in the market.
"The Deputy President must have been speaking to the number of bags that were awarded to this firm to supply. The first consignment of this contractor was 50,000 bags,'' the CS clarified.
Gachagua had said that only 50,000 bags out of the 4 million bags of fertiliser that were imported ahead of the planting season failed to meet the set quality standards.
"The issue of fake fertiliser is a small issue because the quantity involved is negligible,'' Gachagua said when he met Kenyans living in Rwanda.
"We have imported over 4, million bags, but only 50,000 bags were brought by a crooked supplier.''
The DP said that out of the many suppliers who were given contracts, only one who brought in the 50,000 bags had "something that is not acceptable.''
But the CS clarified that the most important thing at the moment is that the government has moved swiftly to address the mess and asked farmers with substandard fertiliser to return it.
"What I have repeatedly said is that there is substandard fertiliser and not fake fertiliser being supplied to some people outside the government's subsidy programme,'' Linturi said.
