A nine-year-old girl and an 80-year-old man were killed by collapsing walls and a third elderly man in his 80s died under a fallen bookcase.
Thee people have been confirmed dead after a magnitude-6.1 natural disaster struck Osaka and neighboring prefectures at 7:58 a.m. on Monday.
The quake 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).
The United States Geological Survey (USGS) measured the tremor at magnitude 5.3, struck at a depth of 15.4km.
Officials said the quake also toppled concrete walls and shut off some water supplies.
A number of train services were suspended, including the "shinkansen" bullet train, as multiple smaller aftershocks followed the quake.
Television images showed buildings swaying and burst pipes spewing water after the quake, which struck at the height of rush hour in the city of around two million.
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The weather agency warned that a strong quake with a similar size could jolt the Osaka region within a week, but dismissed concerns that Monday's temblor could trigger a megaquake that is projected to occur in the future off western Japan with massive tsunami.
This is a developing story. There was no damage to its Ohi and Takahama nuclear plants which are both located in the region, Kyodo News reported. "Almost all of the dishes fell and shattered on the floor", said Kaori Iwakiri, a 50-year-old nurse in Moriguchi, just north of Osaka city. At least 234 people were injured, public broadcaster NHK said.
Local officials said they had not received reports of major damage in the highly urbanised area, where roads and train tracks criss-cross around densely packed apartment buildings.
Japan's JXTG Nippon Oil & Energy Corp has shut all its refining units at the 115,000 barrels per day Osaka refinery after the natural disaster, with product shipments halted.
Some subway service resumed in the afternoon, but stations remained crowded with passengers waiting for trains to restart, many of them sitting on the floor. Japanese media reported one of the likely victims is a 9-year-old girl at a school.
Japanese authorities don't confirm death until after an examination at a hospital.
In the hours following, more than 170,000 homes remained without power in Osaka, while almost 700 Hyogo households were left in the dark, Kansai Electric Power Company told NHK.