A powerful quake that jolted northern Osaka Prefecture on June 18, leaving at least three dead and dozens injured, occurred near a major active fault zone, the Japan Meteorological Agency (JMA) said.
Local officials also issued a warning against spreading fake news online after a tweet claiming a zebra was on the loose after the quake went viral.
Prime Minister Shinzo Abe said the government was assessing damage and that its top priority was the safety of residents. At least 200 people have been injured, Kyodo News reported.
About 850 people took refuge at some 400 shelters in Osaka Prefecture, with many concrete block walls and other structures damaged by the quake.
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 struck shortly after 8 a.m. north of Osaka at a depth of about 13 kilometers, the Japan Meteorological Agency said.
The quake struck an important industrial area of central Japan.
The company said it was halting production at three of its plants. Daihatsu Motor Co, a unit of Toyota Motor Corp, stopped its factories in Osaka and Kyoto while it checked for damage.
Dozens of flights were grounded and trains were halted, although some resumed operation by Monday evening.
Tractor maker Kubota Corp. said it halted two plants in the area, while air conditioner maker Daikin Industries Ltd suspended operations at two plants, one of which had restarted by noon.
The natural disaster reminded numerous magnitude 7.3 Kobe quake in 1995 that killed more than 6,000 people in the region.
Three people were confirmed dead, including a nine-year-old girl, who was reported to have died after a school wall fell on her. Another man in his 80s was killed when a bookcase fell on him. While the natural disaster was centered near Osaka, it affected a large portion of western Japan.
"It was only slight at first, then after a few seconds everything shifted from side to side and I realised I was experiencing an quake".
"I didn't know what was happening", Daniel said. "The whole world was aggressively shaking", she said.
Nishino said he and players found out about the natural disaster shortly after it happened because an alarm went off at the team hotel in Saransk and blared for about 15 minutes around the same time as the quake struck.
The Osaka prefectural government reported two deaths, and an Ibaraki city official confirmed a third. Earlier that day he'd stopped with friends at Osaka train station. Television images showed passengers getting off trains onto the tracks between stations.
Live footage showed burst water mains and a house on fire after the quake hit Osaka, which will host next year's Group of 20 summit, just before 8 a.m. (2300 GMT Sunday) as commuters were heading to work.
However, the 6.1 magnitude quake did not trigger a tsunami warning and nuclear plants in the area are operating normally.