NEMA has said the ban on plastic bags does not affect flat bags used in industrial packaging.
Director general Geoffrey Wahungu said on Friday industries will still be allowed to use plastic bags as a primary packaging source.
He said the bags will not be available over the counter in shops or to be given freely outside the industrial setting.
"This is to notify the general public that the ban applies to carrier bags with handles and with or without gussets as well as flat bags without handles and with or without gussets," Wahungu said.
Wahungu said bags used in packaging must be labelled by the firm manufacturing the product to ensure there is full compliance.
There has been outcry from manufacturers following a gazette notice banning the use of plastic bags from September this year.
"The ministry has banned the use, manufacture and importation of all plastic bags used for commercial and household packaging," the Environment CS said in the notice dated February 27.
Manufacturers warned that the ban will lead to the loss of about 60,000 jobs directly, and another 400,000 indirectly.
Through their lobby, the Kenya Association of Manufacturers, the industries pleaded with the government to consider their proposal for a waste management programme through the Finance Bill 2017.