The California Department of Pesticide Regulation says the state has not determined the products are safe.
The suit was filed Monday in Sacramento Superior Court, and seeks a court order requiring the grocer to explain why it is selling pesticide products that do not comply with state safety laws.
The products are 365 Natural Pines Pellet Cat Litter; Purely Botanical Cat Flea Spray; Purely Botanical Dog Flea Spray and Enviroman Bugs R Done Bug spray.
Whole Foods said it cooperated fully with the department and looked forward to addressing the matter before a judge.
If it is found to have sold unregistered pesticides, the state could issue fines.