Four people are feared killed and over 100 injured in the storm, which triggered landslides and snarled transportation.
The warning is issued only when it forecasts conditions seen once in several decades.
Several thousand people have been evacuated from their homes due to the flooding exacerbated by Typhoon Nanmadol. Rescue operations are continuing and the death toll may rise.
At least 100,000 ordered to evacuate their homes as heavy rains batter southwestern Japan. Typhoon Nanmadol slammed Japan on Tuesday, grounding dozens of flights.
The season's third typhoon made landfall in Nagasaki prefecture. At least three people have been injured and up to 47 domestic flights were cancelled.
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