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More than 75,000 residents in the prefectures of Kumamoto and Kagoshima were urged to evacuate following pounding rains overnight.
The evacuation was not mandatory and it was not known how many fled.
“I smelled mud, and the whole area was vibrating with river water. I’ve never experienced anything like this,” a man in a shelter in Yatsushiro city, in western Kumamoto, told NHK TV. He said he fled early fearing a disaster.
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Mudslides smashed into houses and floodwaters carried trunks from uprooted trees. Several people were standing atop a convenience store as they waited for rescuers.
Kumamoto Governor Ikuo Kabashima later told reporters that 14 residents at a flooded elderly care home in Kuma village were presumed dead after being found during rescue operations, according to Japanese media including NHK and Kyodo News.
Officials said they were still sorting out the numbers and could not confirm the toll.
In Tsunagimachi district, two of three people buried underneath mudslides were pulled out without vital signs, Kumamoto prefectural crisis management official Takafumi Kobori said. Rescuers were still searching for the third person.
In another badly flooded town, Ashikita, six people were unaccounted for and a seventh was seriously injured, Kumamoto officials said.
In the mountainous village of Kuma, residents stranded at their homes were being airlifted by a rescue helicopter.
In Hitoyoshi city, rescuers transported some residents in a boat. Flooding also cut off power and communication lines.
About 8,000 homes in Kumamoto and neighbouring Kagoshima were without electricity, according to the Kyushu Electric Power Co.
Flooding also cut off power and communication lines.
Prime Minister Shinzo Abe set up a task force and said up to 10,000 defence troops were being mobilised for rescue operations.
The Japan Meteorological Agency earlier issued warnings of extraordinary rain in parts of Kumamoto, which is about 1,000 kilometres (600 miles) southwest of Tokyo, but later downgraded them as the rainfall estimated at 100 millimetres (4 inches) per hour.