More than one million people in Kagoshima remained under evacuation order on Thursday morning, with additional orders being issued along with lower-level evacuation advisories.
Kagoshima city, Kirishima and Aira, in Kagoshima prefecture on Kyushu island, urged their residents to move to safety immediately.
Torrential rains have created risky conditions in southwestern Japan, prompting evacuation orders for more than 1.1 million people in the Kyushu region, according to state broadcaster NHK News.
Heavy rains since Saturday have caused landslides at 43 areas in the nation, mainly the Kyushu region, the land ministry said Thursday.
At least four people were injured during the severe weather, while dozens of homes have been damaged and hundreds left without power.
The worst affected areas are the southernmost main island of Kyushu which received as much as 40 inches (1,000 mm) of rain, or more than double the usual volume for all of July according to public broadcaster NHK.
In one case a auto flipped onto its side in a mudslide, injuring a woman and her child, NHK said.More news: Beijing backs criminal probe into ‘illegal actions’ of Hong Kong protesters
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Some 14,000 troops have been placed at the ready for necessary rescue work.
The severe weather front could hover over Japan until Saturday, and is also expected to hit parts of eastern Japan, the JMA said.
The Japan Meteorological Agency has warned that life-threatening landslides are possible at any time in parts of Kagoshima, adding heavy rain will continue overnight.
For the 24 hours through noon Friday, the agency forecast up to 120 mm of rain on Tanegashima and Yakushima islands in Kagoshima, 100 mm in the Kanto-Koshin region and 70 mm in the Tokai region.
From early June to late July, Japan traditionally experiences a rainy "baiu" season, as humid air from the south converges with cooler, drier air from the north.