The upscale grocer last month disclosed card information had been stolen from taprooms, restaurants and other venues located within some of its stores.
Whole Foods, which Amazon recently purchased for $13.7 billion, said transactions on Amazon.com had not been impacted.
The investigation found unauthorized software was present on the point-of-sale systems at certain venues, the company said.
(Reporting by Karina Dsouza in Bengaluru; Editing by Shounak Dasgupta)