The quake, which had a 6.1 magnitude, hit at 7:58 a.m.
Television footage also showed a "shinkansen" bullet train stopped on the railway.
The inland natural disaster, with a preliminary magnitude of 6.1, occurred at a depth of around 13 kilometers shortly before 8 a.m., with its epicenter in the northern part of Osaka Prefecture in an area where active faults are concentrated.
Two elderly men and one 9-year-old girl died after being hit by collapsing walls and furniture, according to the Japan Times.
There were no immediate reports of major damage and no tsunami warning was issued after the powerful quake, which stranded commuters and left tens of thousands without power.
Kansai Electric Power said no irregularities had been detected at the Mihama, Takahama and Ohi nuclear plants after the quake.
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Monday's quake was of a relatively low magnitude, but registered up to a lower-6 on the Japanese seismic intensity scale of 0 to 7.
The prime minister, Shinzo Abe, said the government was assessing the damage and that its priority was to rescue anyone trapped inside buildings.
"There are fears that the risk of house collapses and landslides has increased in the areas shaken strongly", said Toshiyuki Matsumori, in charge of monitoring quakes at the agency.
While the quake appeared to spare the region of major infrastructural damage, the Meteorological Agency warned that strong aftershocks could occur, particularly in the next two to three days. An 84-year-old man in nearby Ibaraki died when a bookshelf fell on him at home, city officials say.
Kate Kilpatrick, visiting Japan for the first time from the United States, said alarms went off nearly immediately in the Osaka hotel she was staying and a loudspeaker told guests to stay away from windows.
"It was not as bad as the Kobe quake", he told the Associated Press from Osaka.