Otsuka Beverage Co Ltd. said in a statement that the recalled water posed no health threat, and the Crystal Geyser bottles may have absorbed smells during the summer when they were kept in storage for a long time.
Kyodo News agency, meanwhile, said an estimated 8 million bottles would be recalled.
Consumers complained the Crystal Geyser smelled like medicine or pesticide, prompting the company to recall the water bottles, Kyodo said. The firm's statement did not give details, including how many bottles it planned to recall. Company officials could not be reached for comment late Monday.
Japan has been hit by several high-profile incidents involving tainted food, including rice and soybeans, and Tokyo is considering creating a new, specialized agency to monitor food and product safety.
In October, a major Japanese instant noodle maker issued a nationwide recall after a woman got sick when she ate a cup of noodles that was later found to be tainted with an insecticide.
Another Japanese trading company also recalled a popular dessert imported from China in October after finding chemical contamination in the custard-filled tarts.