Forecasters said: "Heavy rainfall will occur during the period indicated with the potential for heavy downpours locally and during shorter intervals.
"There is potential for flooding on already saturated or waterlogged grounds."
The warning is valiid from Sunday 13 October at 6pm to Monday 14 October at 11.59pm.
Meanwhile, Japan has deployed tens of thousands of troops and rescue workers after one of the strongest storms in years hit, killing at least 18 people.
Typhoon Hagibis made landfall south of Tokyo on Saturday, moving north and bringing severe flooding.
Thirteen people are missing from the storm, public broadcaster NHK said.
In the Nagano area, water surrounded Japan's famous bullet trains while helicopters plucked stranded residents from rooftops.
A total of 27,000 military troops and other rescue crews have been deployed in relief operations, authorities said.
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