Public broadcaster NHK said that in addition to the dead, more than 230 people were injured.
More than 170,000 homes were without power as of 9.50am, regional utility Kansai Electric Power said, although there were no reports of abnormalities at its nuclear plants in the region.
The quake knocked over walls, broke windows and set off scattered building fires.
Shinkansen bullet train services have been partly halted.
A strong 6.1 magnitude quake has knocked over walls and set off scattered fires around metropolitan Osaka in western Japan, killing at least three people and injuring dozens.
The Osaka prefectural government reported two deaths, and an Ibaraki city official confirmed a third.
The natural disaster struck with a magnitude of 5.9 at 7:58 a.m. local time, at a depth of 10 kilometers (6.2 miles).
The magnitude 6.1 quake struck the city of Osaka and the surrounding area Monday about 8 a.m.
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A strong magnitude 6.1 quake struck the city of Osaka and the surrounding area on Monday morning.
The Fire and Disaster Management Agency said one person had no heartbeat and wasn't breathing and a second person also had no vital signs.
Japanese broadcaster NHK reported the girl was on her way to school at the time.
The victims, who have yet to be named, were described as being in a state of "cardiopulmonary arrest" - a term Japanese media use until doctors have conducted formal examinations. The Japan Meteorology Agency put the magnitude at 5.9 and JMA Seismic Intensity at 5.3.
"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.
However, there was no large-scale destruction and no tsunami warning issued after the quake, although commuters were stranded and tens of thousands were left without power.
Local police also told AFP that they had not received reports of substantial damage, and the Nuclear Regulation Authority said it had detected no abnormalities at its facilities after the quake.