Most of the deaths have occurred in Hiroshima prefecture, which has been hit by torrential rain since Thursday.
The rains are the deadliest weather disaster in Japan since two typhoons that hit back-to-back in August and September 2011, killing almost 100 people.
Torrential rains have pounded western parts of the country with three times the usual precipitation for this time of the year, setting off landslides and causing rivers to breach their banks. In another area in Hiroshima, 12 people went missing when a residential area got sucked into a landslide, and one body was later found.
In western Okayama prefecture, rescue operations were underway to evacuate several hundred people including children and the elderly from a hospital, some by helicopter.
The Department of International Relations and Cooperation (Dirco) said the South African Embassy in Japan had not reported any South African victims and remained in close contact with the Japanese authorities.
According to the transport ministry, 17 railroad operators were suspending services on 56 routes in western Japan or elsewhere.
Several major manufacturers, including carmakers Daihatsu and Mitsubishi, suspended operations at plants in the affected areas.
Two million people have been ordered to evacuate following flash floods and landslides in Japan, which has claimed at least 80 lives.
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The death toll was put at 38 this morning by the public broadcaster NHK, with dozens more missing.
In Motoyama, a town on Shikoku island about 600 km from Tokyo, 583 millimetres (23 inches) of rain fell between Friday and Saturday mornings, the Meteorological Agency said. Majority were rescued by boat or helicopter.
Evacuation orders remained in place for some 2 million people and another 2.3 million were advised to evacuate, although rain had stopped and floodwaters retreated in some areas.
Hiroshima prefecture has been severely affected by rains. "This is a situation of extreme danger".
Military water trucks were dispatched to areas where water systems were no longer working, Okayama prefecture said. "There are still many people who have been unaccounted for".
The JMA is urging people to stay vigilant and listen out for emergency alarms from local governments issuing advisories or calling for immediate evacuations.
An overturned auto remains on a street after heavy rain in Ozu, Ehime Prefecture, Japan.
The toll has risen steadily since then, and the conditions have made rescue operations hard, with some desperate citizens taking to Twitter to call for help. Critical infrastructure has been hit, including railway tracks.