No tsunami warning was issued.
Prime Minister Shinzo Abe told reporters the government was "working united, with its first priority on saving people's lives". About 150 people were injured, the broadcaster NHK said, lowering an earlier toll after a revision by city officials. Kansai also said more than 170 000 households were without power in Osaka and neighboring Hyogo prefecture.
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.
The magnitude 6.1 quake near the major city of Osaka killed three people, toppled concrete walls and store shelves and temporarily knocked out some power and water supplies.
In April 2016, two earthquakes struck Kumamoto with the first quake, a 6.2 magnitude quake, followed one day later with a bigger tremor hitting a wider area and measuring 7 on the Richter scale.
The quake struck an important industrial area of central Japan.
The quake forced the temporally closure of many businesses and plants in the area, including Panasonic and Daihatsu Motor Co, a unit of Toyota Motor Corp.
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. Long lines of people waited to board bullet trains as they resumed operation.
The natural disaster reminded numerous magnitude 7.3 Kobe quake in 1995 that killed more than 6,000 people in the region.
Two elderly men and one 9-year-old girl died after being hit by collapsing walls and furniture, according to the Japan Times. Another man in his 80s was killed when a bookcase fell on him.
The quake, which struck at around 7:58 a.m. Monday, is believed to have occurred at a depth of about 13 kilometers in the northern part of the prefecture, the Japan Meteorological Agency said.
Kilpatrick, visiting Japan for the first time, said alarms went off nearly immediately in the hotel and a loudspeaker told guests to stay away from windows.
"It was so terrifying because this is my first natural disaster".
"The whole building was shaking, I was so scared, telling myself 'Gloria this is it, your time is up.' Finally the [shaking] stopped", she told the BBC. The epicentre of Monday's quake, which the JMA said occurred at a depth of 13km, was about an hour to the north of the main entertainment district of Dotonbori.
The two other victims were an 80-year-old man in the city of Osaka, who was hit by a collapsed wall, and an 85-year-old man in Ibaraki in the same prefecture who was trapped under a bookshelf, the police said.
Passengers get off a train which suspended its service in Osaka, following an quake Monday, June 18, 2018. Television images showed passengers getting off trains onto the tracks between stations.
Osaka prefecture, which includes the city and surrounding areas, has a population of 8.8 million.