Two men in their eighties died in Osaka City and in Ibaraki, and a nine-year-old girl was killed in the city of Takatsuki in western Japan on Monday morning, according to Japan's Fire and Disaster Management Agency.
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.
Meantime, a 5.6 magnitude quake struck near Guanagazapa in Guatemala's Escuintla province just after 8:30 p.m. local time (10:30 p.m ET) Sunday, according to the USGS. The strongest shaking was in an area north of Osaka city.
Japan does not confirm deaths until a formal examination has been made and generally uses the term cardiopulmonary arrest in such cases.
The quake disrupted some of Japan's usually meticulous train services from Osaka to other major cities including Tokyo and Nagoya.
A strong quake knocked over walls and set off scattered fires around metropolitan Osaka on Monday morning. The jolt struck during the Monday morning rush hour, and forced a halt to some rail services. The inland natural disaster poses no tsunami risk.
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. There were no reports of abnormalities at its nuclear plants in the region.
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Footage on national broadcaster NHK showed flooding from burst underground water pipes, train passengers forced to exit along train lines, and schoolchildren gathering outside in precautionary evacuations.
Multiple small aftershocks followed the quake, and an official from Japan's meteorological agency warned residents to remain on guard.
Daihatsu Motor Co, an Osaka-based unit of Toyota Motor Corp, said it had suspended production at its factories in Osaka and Kyoto while they check for damage.
Prime Minister Shinzo Abe told reporters the government was "working united, with its first priority on saving people's lives".
In a 1995 deadly quake in the region, which had a magnitude of 7.3 and recorded 7 on the Japanese seismic intensity scale, 6,434 people were killed.