The magnitude 6.1 quake struck north of Osaka city Monday shortly after 8 a.m.
"There have been no reports of substantial damage so far although we are still checking the situation", an official at Osaka prefectural police told AFP.
The morning commute was disrupted as train and subway service in the Osaka area including the bullet train were suspended to check for damage to equipment.
Private broadcaster TV Asahi showed firefighters responding to a blaze that broke out after the quake at a house north of Osaka city. The temblor had an intensity of lower 6 on the Japanese scale of 7.
The vehicle manufacturer Daihatsu said it had suspended operations at its plants in Osaka and nearby Kyoto, while the consumer electronics firm Sharp said its factories were operating normally.
One victim was a 9-year-old girl who was knocked down by a concrete wall at her elementary school as she walked by.
An American visitor to the city described being woken up by violent shaking.
The quake struck in one of Japan's main manufacturing heartlands, home to companies including Panasonic Corp., Nintendo Co. and Keyence Corp, and plants across the area were halted as firms assessed the damage.
"It was so terrifying because this is my first quake".
Meanwhile, Japan's JXTG Nippon Oil & Energy Corp says it has shut all refining units at its 115,000 barrels-per-day (bpd) Osaka refinery after the quake. More than 170,000 households in Osaka and neighboring Hyogo prefecture lost power temporarily but it was restored within two hours, the utility said.
Honda Motor Co. said production in Suzuka, in nearby Mie prefecture, was halted for checks but no problems were found and operations were back to normal.
A massive magnitude 9.0 quake hit northeastern Japan on March 11, 2011, triggering a huge tsunami that killed some 18,000 people and triggered the world's worst nuclear disaster in a quarter of a century at Tokyo Electric Power's Fukushima Daiichi nuclear plant.