The heavy rains triggered massive landslides in some areas: "There have been massive flooding and landslides", government spokesman Yoshihide Suga told a news conference.
On Saturday morning, the Japan Meteorological Agency lifted special rain warnings issued the previous day for Hiroshima and Tottori prefectures in the Chugoku region and Fukuoka, Saga and Nagasaki prefectures in the Kyushu region.
As of Saturday, at least 67 people were missing with the majority in Hiroshima, 47, while others were unaccounted for in Ehime and Okayama Prefecture.
Scientists have warned that one effect of global warming could be an increase in rain-related disasters, and experts now say people should leave well in advance of evacuation orders where forecasts show heavy rain is possible.
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Kyodo reported several deaths in a landslide in Hiroshima and more bodies were retrieved from collapsed housing in the ancient capital of Kyoto, both areas where the rainfall was heavy in the past few days.
Shinzo Abe, Japan's prime minister, warned of a "race against time" to rescue victims of torrential rainfall that has killed more than 81 people. Majority were rescued by boats or helicopters.
The agency is also maintaining the same warning that has been issued to Gifu Prefecture.
"I have asked my family to prepare for the worst", said Kosuke Kiyohara, 38, as he waited for word of his sister and her two young sons.
Elderly residents look at half submerged homes in floodwater from heavy rains, in Kurashiki, Okayama prefecture in southwestern Japan.
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The government has set up an emergency management centre at the prime minister's office.
Japanese soldiers rescued people by boat in Hiroshima, while others were rescued from rooftops by helicopters.
Flash floods and landslides across central and western areas have sparked evacuation orders for more two million people.
Okayama prefecture said in a statement that four people had died, eight others were missing and 11 were injured, at least one of them seriously. Hundreds of homes have been damaged. Some automakers halted production as the rain and flooding disrupted supply chains and risked workers' safety, Kyodo news agency reported.
Roads were transformed into muddy flowing rivers, with dirt piled up on either side and stranded cars barely withstanding the current flowing around their wheels.
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At the moment a team of 54,000 rescuers composed of members of the military, police and fire departments has been dispatched across the west and southwest of Japan.