Japanese authorities told tens of thousands of people to evacuate the quake-hit northern region of Ishikawa on Saturday as "unprecedented" rains triggered floods and landslides.
A dozen rivers in the region had burst their banks as of 11am (0200GMT), land ministry official Masaru Kojima said.
The cities of Wajima and Suzu, as well as Noto town, ordered about 44,700 residents to evacuate, local officials said.
The Japan Meteorological Agency (JMA) said it issued its highest level warning for Ishikawa, cautioning of a "life-threatening situation".
The areas under the warning were seeing "heavy rain of unprecedented levels", JMA forecaster Satoshi Sugimoto told reporters, adding "it is a situation in which you have to secure your safety immediately".
At least one person was missing in Wajima, while many buildings were inundated, with landslides blocking parts of roadways, the Ishikawa government said in a statement.
Public broadcaster aired footage showing an entire street in Wajima submerged under water.
Three rivers in Ishikawa were overflowing into nearby communities, a local official told earlier.
At least one house was hit by a landslide, the Fire and Disaster Management Agency said, without giving further details.
Another 16,000 residents in Niigata and Yamagata prefectures north of Ishikawa were also told to evacuate, the agency said.
Wajima and Suzu, in central Japan's Noto peninsula, were among the areas hardest hit by a huge New Year's Day earthquake that killed at least 236 people.
The region is still reeling from the magnitude-7.5 quake that toppled buildings, ripped up roads and sparked a major fire.
Japan has seen unprecedented rainfall in parts of the country in recent years, with floods and landslides sometimes causing casualties.
Scientists say human-driven climate change is intensifying the risk of heavy rain in the country and elsewhere because a warmer atmosphere holds more water.
