The 5.3-magnitude quake struck at a depth of 15.4km at 7.58am (6.58am, Singapore time) near Osaka, according to the United States Geological Survey (USGS).
The quake knocked over walls, broke windows and set off scattered building fires.
An natural disaster measuring 4.7 on the Richter scale hit a central part of Japan including Gunma, Ibaraki, Tochigi and Saitama prefectures at around 3:27 p.m. on June 17, the Japan Meteorological Agency said. Japanese media reported one of the likely victims is a nine-year-old girl found at a school.
Local police said they could not confirm the reports. The strongest shaking was in an area north of Osaka city, the agency said.
Prime Minister Shinzo Abe told reporters the government was "working united, with its first priority on saving people's lives". It toppled book shelves in homes and scattered goods on the floor of convenience stores and other shops.
The operation of bullet trains running through the prefecture was suspended following the quake but service was resumed shortly afterward after no safety problems were detected. Television images showed passengers getting off trains onto the tracks between stations.