Meantime, on the other side of the Pacific, 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. Television images showed passengers getting off trains onto the tracks between stations.
The natural disaster 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).
NHK said an 80-year-old man had also been killed by a collapsing wall, and that the third fatality was a man trapped under a bookcase in his home.
A nine-year old girl killed by a falling wall at her school was one three confirmed fatalities.
Osaka prefecture, which includes the city and surrounding areas, has a population of 8.8 million.
Both the high-speed Shinkansen and local trains suspended operations during the morning commuting hours.
Kansai Electric Power said no irregularities had been detected at three nuclear plants in the region.
A lower 6 on the Japanese seismic intensity scale of 7 was registered in Kita Ward, Osaka as well as Takatsuki, Hirakata, Ibaraki and Minoo in the prefecture.
Prime Minister Shinzo Abe said the government was assessing damage and that its top priority was the safety of residents.
The strongest shaking unfolded in an area north of Osaka city, the agency said.
Kate Kilpatrick, visiting Japan for the first time from the United States, said alarms went off nearly immediately in the Osaka hotel she was staying and a loudspeaker told guests to stay away from windows.
Market reaction to the event was largely muted, with shares in some companies located in the region including Osaka Gas dropping, while Sumitomo Osaka Cement Co. and electrical contractor Kinden Corp. gained as the extent of damage from the quake remained unclear.
"We were sleeping and it woke us up abruptly", she said.