Students sit on a playground after they were evacuated from school building after an quake at Ikeda elementary school in Ikeda, Osaka prefecture, western Japan, Monday. Kansai also said more than 170,000 households were without power in Osaka and neighboring Hyogo prefecture.
The train and subway service in and around Osaka, including the bullet train to Tokyo, was suspended while checks were made.
The Japan Meteorological Agency said no tsunami warning has been issued yet.
NHK and other Japanese media said collapsing walls had killed an 80-year-old man and a 9-year-old girl, and that another man in his 80s was killed after being crushed by a toppling bookcase.
"At this point we have information that two people died", he told reporters, adding that 20 people had been injured.
There was no risk of tsunami from the tremor, the Japanese meteorological agency said, putting its magnitude at 5.9, and the epicentre at a depth of 10km.
Senior government officials are gathering for an emergency meeting at the Prime Minister's office, broadcaster NHK reported.
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Live footage showed burst water mains and a house on fire after the quake hit Japan's second-biggest metropolis just before 8am (2300 GMT Sunday) as commuters were heading to work.
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.
A lower 6 on the Japanese seismic intensity scale of 7 was registered in Kita Ward, Osaka as well as Takatsuki, Hirakata, Ibaraki and Minoo in the prefecture. In 1995, a magnitude 6.9 quake killed more than 6,000 people when it struck in neighboring Kobe.
"I was stunned. I couldn't do anything", he told AFP from Itami, a city in eastern Osaka region.
In a quake with an intensity of lower 6, it is hard to remain standing and unsecured furniture may move or topple over, according to the agency. "I was very scared", said 64-year-old Katsufumi Abe, who was at JR Osaka Station on his way to Kyoto.
It also sent three reactors into meltdown at the Fukushima nuclear plant, causing Japan's worst postwar disaster and the most serious nuclear accident since Chernobyl in 1986.