The Fire and Disaster Management Agency said 214 people were treated for injuries in hospital, majority in Osaka - Japan's second city.
The magnitude 6.1 quake struck north of Osaka city Monday shortly after 8 a.m.
The Fire and Disaster Management Agency said the number of the injured had risen to 91 about three and a half hours after the quake struck the region.
One victim was a nine-year-old girl who was knocked down by a concrete wall at her elementary school as she walked by.
Japan does not confirm deaths until a formal examination has been made and generally uses the term cardiopulmonary arrest in such cases.
Media reported she had been trapped when a wall collapsed on her at school following the 6.1-magnitude quake.
The shinkansen bullet train service remains halted due to the quake as at 11.30am local time, while the Hanshin Expressway that connects Osaka to the neighbouring Kyoto and Kobe cities is also closed. Television images showed passengers getting off trains onto the tracks between stations.More news: All of Mexico cheers win over champ Germany
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Kansai Electric said on its website that around 170,000 homes in the Osaka region were briefly left without power.
The quake knocked over walls, scattered goods on the floor of shops and set off scattered fires around Osaka. Books were thrown off the shelves at a store. Train service was suspended across a wide area during the morning commute.
Although largely unaffected by the powerful quake, Chan said groups may need to adjust their itineraries.
Prime Minister Shinzo Abe told reporters the government was "working united, with its first priority on saving people's lives". Mitsubishi Motors briefly shut down production at two plants in Kyoto and Shiga prefectures, while Daihatsu Motor Co, a subsidiary of Toyota Motor Corp, suspended operations at two plants in Osaka and Kyoto prefectures. The quake also grounded flights in and out of Osaka, and paralyzed traffic and commuter trains most of the day.
Monday's natural disaster caused fires to break out in the residential Takatsuki City district, while there have been reports of flooding due to burst water pipes. It also cracked roads and broke water pipes, leaving homes without water. I thought it was a nightmare because I was so confused.
Kilpatrick, visiting Japan for the first time, said alarms went off nearly immediately in the hotel and a loudspeaker told guests to stay away from windows.
She said the council had not received any requests for help from Hong Kong travellers regarding the quake. A magnitude 4.6 quake struck Gunma prefecture - north of Tokyo - on Sunday, while a magnitude 4.5 tremor hit Chiba - east of Tokyo - on Saturday.