Authorities in Japan use that term before a doctor officially certifies death. About 8,000 homes in Kumamoto and neighbouring Kagoshima were without electricity, according to the Kyushu Electric Power Company. Several people were seen standing on top of a store waiting to be rescued.
More than 75,000 residents in the southern prefectures of Kumamoto and Kagoshima were asked to evacuate following torrential rain overnight.
The rain front that brought the downpour in Kumamoto and Kagoshima, as well as neighboring Miyazaki Prefecture, is expected to straddle large areas of western and eastern Japan through Sunday, the weather agency said.
Haruka Yamada, a resident of the town of Ashikita in Kumamoto, said nearby houses were already flooded when she woke up to the sound of rain around 4 a.m.
Prime Minister Shinzo Abe urged people to be on "maximum alert".
Local media reported that two people in hard-hit Kumamoto, who had been buried by a landslide, showed no life signs. Rescuers were still searching for the third person. Kumamoto officials said they were still assessing the extent of the damage.
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Fourteen of those found without vital signs were at a nursing home in Kuma village, where water and mud gushed into the building.
The warning also targeted local communities bracing for heavy rainfall caused by a line of rain clouds stalling over the area.
The warnings cover the Kumamoto cities of Yatsushiro, Amakusa and Hitoyoshi, and parts of Kagoshima, including the cities of Akune and Isa.
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Tens of thousands of people have been told to evacuate homes.
The Kuma River, which flows through the Kumamoto prefecture has risen well above its banks, washing away at least one bridge and cutting off citizens from rescue crews. "I've never experienced anything like this", a man in a shelter in Yatsushiro city in western Kumamoto told national Japanese broadcaster NHK. They had previously said two were feared dead.
Officials said that about 10,000 Self-Defense Forces members were preparing to be sent to the Kyushu region.
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Japan is now in its rainy season, which often causes floods and landslides and prompts local authorities to issue evacuation orders.