The outlets will remain open to facilitate the ongoing planting season.
Linturi urged farmers to continue purchasing the subsidised fertiliser.
The ministry had earlier refuted reports that some farmers have been supplied with sub-standard fertiliser.
Farmers across the country will continue to access subsidised fertiliser and seeds during the Easter holiday to facilitate the ongoing planting season.
The development comes after Agriculture Cabinet Secretary Mithika Linturi directed all National Cereals and Produce Board (NCPB) and Kenya Seed Company outlets countrywide to remain open during the holiday.