The Auckland-based company, which makes natural laundry and dish-cleaning products, said it had taken the product off shelves.
It reassured customers that the disinfectant was not dangerous but "just doesn't work as well as we'd like".
"We were disappointed recently to discover that our disinfectant falls short of the 99.9 per cent germ kill claim on the pack," Earthwise said in a statement.
"We're working really hard to reformulate and bring you an improved formula that meets your expectations of Earthwise really soon."
People who have bought the product could take it back to where they bought it for a full refund.
"It's ok to tip it down the sink if you'd prefer," Earthwise said.
The Earthwise Disinfectant Eucalyptus & Thyme 1L (Barcode 9421027310469) is being sold at New World, Pak n Save and Countdown Stores nationwide.