Asahi Breweries Ltd. said it was voluntarily recalling four brands of "imo shochu", a popular liquor produced mostly from sweet potatoes, at a cost of about 1.5 billion yen (14 million dollars).
The rice was used since June in the process of fermenting sweet potatoes for the spirits.
"We have not detected any traces of agrochemical residues in end products," a company spokesman said, adding that the recall was aimed at dispelling consumer worries.
Asahi was the first major beverage company to be hit by a scandal involving a rice processing company, Mikasa Foods, which has resold non-edible rice it had purchased from the government for industrial use.
The products were part of rice imported by the Japanese government from China, Vietnam and other countries under its international commitment to open its rice market.
The rice had been set aside as a problem product after it was found to be contaminated with excessive levels of toxins, or deteriorated with fungi, or affected by other factors in storage.
The government sold the products to private dealers on condition that they be resold for industrial use, such as making glue, but not for human consumption.
But the farm ministry said this week that Mikasa had sold the tainted rice to distillers as well as makers of snacks, such as Japanese rice crackers, in hopes of making more profits.