At least 234 people were injured, public broadcaster NHK said.
"There have been no reports of substantial damage so far although we are still checking the situation", an official at Osaka prefectural police told AFP. Another man, 85, died from a falling bookshelf, while another 80-year-old passed away after being struck by part of a wall.
The Japan Meteorological Agency warned residents of Osaka and surrounding prefectures June 18 to brace for strong aftershocks over the coming week following the magnitude-6.1 natural disaster that rocked the region around the morning commute.
Train guide electric boards tilt following an natural disaster at Ibaraki-shi Station in Ibaraki City, north of Osaka prefecture on June 18, 2018. Japanese authorities don't confirm death until after an examination at a hospital.
Osaka prefecture, which includes the city and surrounding areas, has a population of 8.8 million.
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.
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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.
The morning commute was disrupted as train and subway service in the Osaka area including the bullet train were suspended to check for damage to equipment.
The quake struck in one of Japan's main manufacturing heartlands, home to companies including Panasonic Corp., Nintendo Co. and Keyence Corp, and plants across the area were halted as firms assessed the damage. Some 170,000 homes suffered temporary power outages, which were resolved within hours after the quake, according to Kansai Electric co. Vehicle makers Honda, Mitsubishi, Toyota and Daihatsu all stopped production at plants in the region.
A major quake has always been feared in the area, which is located near several major faults.
Senior government officials are gathering for an emergency meeting at the Prime Minister's office, broadcaster NHK reported.