More than 75,000 residents in the southern prefectures of Kumamoto and Kagoshima were asked to evacuate following pounding rains overnight.
Heavy rain in southern Japan triggered flooding and mudslides on Saturday, leaving more than a dozen missing and others stranded on rooftops waiting to be rescued, officials said.
NHK television footage showed large areas of Hitoyoshi town in Kumamoto inundated in muddy waters that gushed out from the Kuma River. Many cars were submerged up to their windows.
Mudslides smashed into houses and floodwaters carried trunks from uprooted trees. Several people were standing atop a convenience store as they waited for rescuers.
In the Tsunagimachi district, two of three people buried underneath mudslides were pulled out without vital signs, Kumamoto prefectural crisis management official Takafumi Kobori said.
14 feared dead at nursing home
Fourteen people were feared dead after a nursing home was flooded in western Japan, a local governor said.
The victims were found "in cardio-respiratory arrest" at the facility for elderly people that was inundated after a nearby river broke its banks, governor Ikuo Kabashima from the western region of Kumamoto told reporters.
Authorities in Japan use that term before a doctor officially certifies death.
75,000 ordered to evacuate as heavy rain lashes western Japan
Some 75,000 people were ordered to evacuate in western Japan, leaving scores stranded and 13 missing, according to local media and officials.
The nation's weather agency issued the highest emergency level of heavy rain warnings to Kumamoto and Kagoshima on Kyushu island.
Rescuers were searching for three people in Kumamoto after a landslide buried their house, public broadcaster NHK said.
"We have issued evacuation orders after record heavy rain," said Toshiaki Mizukami, an official of Kumamoto prefecture.
"We strongly urge people to take action to protect their lives as it's still raining quite heavily," he said.