The carmaker will resume operations at the Hofu No.1 plant, where it makes the Mazda3, from 8:15 p.m. (1115 GMT) and at the Hofu No.2 plant, where it manufactures the Mazda3 and Mazda6, at 5:00 p.m. (0800 GMT), said spokesman Makoto Watanabe.
The impact on vehicle production has been minor, Watanabe said, but declined to disclose details. Mazda has conducted safety checks and no damage has been found, he said.
An earthquake of magnitude 6.3 struck off Japan's southern island of Kyushu near the city of Oita, the US Geological Survey said.