The Fire and Disaster Management Agency said 214 people were treated for injuries in hospital, a lot of them in Osaka - Japan's second city.
The Japan Meteorological Agency originally put the quake's magnitude at 5.9 but later raised it to 6.1.
The quake collapsed walls and damaged roofs, with the nine-year-old girl killed after she was trapped by a damaged wall at a swimming complex north of Osaka.
Following the magnitude-6.1 quake, Panasonic Corp stopped operations at two plants in Osaka Prefecture as some workers were unable to get to work due to traffic disruption.
The train and subway service in and around Osaka, including the bullet train to Tokyo, was suspended while checks were made. Passengers exited trains on the tracks between stations.
Gas has been cut off to more than 100,000 households in Osaka, while some 170,000 houses in Osaka and neighbouring Kyoto and Hyogo prefectures are left without power.
Scattered fires broke out in buildings in the heavily urbanised area, and while authorities reported no damage to railways or major roads, parts of the network had been closed as a precaution. It toppled book shelves in homes and scattered goods on the floor of convenience stores and other shops.
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Senior government officials are gathering for an emergency meeting at the Prime Minister's office, broadcaster NHK reported. The quake also grounded flights in and out of Osaka, and paralyzed traffic and commuter trains most of the day.
The auto 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.
Myotokuji temple is destroyed by an quake registering a weak 6 on the Japanese seismic scale in Ibaraki City, the north side of Osaka Prefecture on June 18, 2018.
Passengers get off a train which suspended its service in Osaka, following an natural disaster Monday, June 18, 2018.
NHK showed footage of firefighters tackling a blaze that ripped through a home north of Osaka, and several broadcasters showed images of water gushing into the street from underground pipes.
"It was so terrifying because this is my first quake. The whole world was aggressively shaking", she said.
Kilpatrick, visiting Japan for the first time from the United States, said alarms went off nearly immediately in the hotel and a loudspeaker told guests to stay away from windows. 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.