At least two people, including a child, were killed on Monday, after a strong quake rocked the second city of Osaka during the morning rush hour, Japan's government said.
Top government spokesman Yoshihide Suga confirmed the deaths of a child and a man, and said a third person was also feared dead in the quake.
"At this point we have information that two people died," he told reporters, adding that 20 people had been injured.
Local police said the child was a nine-year-old girl who died in the city of Takatsuki, north of Osaka city, with media reporting she was trapped when a wall collapsed on her at school following the 5.3-magnitude quake.
Public broadcaster NHK said the man was an 80-year-old who had also been killed by a collapsing wall, and that the third fatality was a man trapped under a bookcase in his home.
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.
Prime Minister Shinzo Abe told reporters the government was "working united, with its first priority on saving people's lives".
'Ring of fire'
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.
NHK showed footage of firefighters tackling a blaze that ripped through a home north of Osaka, and several broadcasters showed images of water gushing into the street from underground pipes.
The quake struck at 8:00 am, as platforms would have been heaving with passengers waiting to board their commuter trains to work.
A number of train services were suspended, including the "shinkansen" bullet train.
The Nuclear Regulation Authority said it had detected no problems at its local atomic power plants, but some companies, including Honda, said they had suspended operations at local plants.
Kansai Electric said on its website that around 170,000 homes in the Osaka region were without power.
Despite its relatively low magnitude, the quake caused quite a shake, registering a lower six on the Japanese experiential scale of up to seven, meaning it is hard to stay standing.
"The floor moved violently. It was a strong vertical jolt. Nearly 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.
"My parents suffered a blackout and they have no water. I plan to take water to them now."
Eiji Shibuya, 52, said the tremor reminded him of the devastating 1995 Kobe earthquake, which killed nearly 6,500 people.
"I was stunned. I couldn't do anything," he told AFP from Itami, a city in eastern Osaka region.
"I was worried about my son as he had just left for his high school. I was relieved when I confirmed he was safe."
Possibility of aftershocks
Multiple small aftershocks followed the quake, and an official from Japan's meteorological agency warned residents to remain on guard.
"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.
And government spokesman Suga also cautioned "there is a possibility that strong aftershocks will happen."
"Large-scale quakes are likely to happen in the next two to three days," he told reporters.
Japan sits on the so-called Pacific "Ring of Fire" where a large proportion of the world's earthquakes and volcanic eruptions are recorded.
On March 11, 2011, a devastating magnitude 9.0 quake struck under the Pacific Ocean, and the resulting tsunami caused widespread damage and claimed thousands of lives.
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.