As the quake was centered inland, there was no fear of a tsunami.
The government confirmed two of the deaths.
Motochika Goto, 85, was crushed by a bookcase and died in Ibaraki in the Osaka suburbs, according to local police.
The Japan Meteorological Agency has updated the magnitude of the quake to 6.1, stronger than the initial 5.9 magnitude.
It also said there were more than 170,000 households without power in Osaka and neighboring Hyogo Prefecture.
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"The government has united to respond (to the disaster) under the policy to put top priority on people's lives", Prime Minister Shinzo Abe said as the government set up an emergency response team. At least 234 people were injured, public broadcaster NHK said.
Water floods out from crack in the road, following an natural disaster in Takatsuki, Osaka, Monday, June 18, 2018.
Roads suffered severe damage and water pipes burst, sending water flowing onto streets of Takatsuki city where the biggest shock was felt. Television images showed passengers getting off trains onto the tracks between stations.
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.
Kepco said its Fukui nuclear plants were operating normally.
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No irregularities were detected at the Mihama, Takahama and Ohi nuclear plants to the north of Osaka, Kansai Electric Power said. At 13 kilometers (8.1 miles) it was relatively shallow, and caused heavy shaking that registered a lower 6 on the Japanese scale of 7.
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.
"Please make sure that you are fully on alert about seismic activities and information on rainfall, and stay clear of risky places".
Both Japan and Guatemala are situated on the Ring of Fire, an area of intense seismic and volcanic activity on both sides of the Pacific Ocean.
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