The natural disaster was recorded at 7.58 a.m. and had its hypocenter at about 13 km depth in Osaka Prefecture on the island of Honshu, the largest in the Japanese archipelago, according to the Japan Meteorological Agency (JMA).
Japanese broadcaster NHK reported the girl was on her way to school at the time.
Some areas in Osaka are reportedly experiencing power shortage.
The Japanese government had not received reports of major damage as of 8.30 am local time (11.30 pm GMT ), spokesman Yoshihide Suga told reporters.
Magnitude 6.1 quake kills three, stops factories in Japan's Osaka area.
The prime minister, Shinzo Abe, said the government was assessing the damage and that its priority was to rescue anyone trapped inside buildings.
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A scale of upper 5 was also registered in Toyonaka, Suita, Neyagawa and Settsu in the prefecture, as well as in Amagasaki in Hyogo Prefecture and Kyoto.
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.
Kansai Electric Power said no irregularities had been detected at three nuclear plants in the region.
The quake disrupted some of Japan's usually meticulous train services from Osaka to other major cities including Tokyo and Nagoya. An 80-year-old man in Osaka City also died after a wall fell on him. "There are fears that the risk of house collapses and landslides has increased in the areas shaken strongly", said Toshiyuki Matsumori of the country's meteorological agency.
Several buildings in Osaka and Takatsuki collapsed and were on fire.
Automakers Honda Motor Co., Mitsubishi Motors Corp. and Toyota Motor Corp. unit Daihatsu all stopped production at plants in the region. The agency added the quake occurred at a depth of about 6 miles (10 kilometers) and no tsunami warning was issued.
"We were sleeping and it woke us up abruptly", Kate Kilpatrick, who was staying in a hotel in Osaka, told Reuters.