Three people are reported to have died as heavy rains pound south-western Japan
Authorities have asked almost one million people to evacuate, warning "unprecedented" levels of rain fall could cause the flooding of rivers, trigger landslides and submerge houses.
"It is a situation where you should do your best to protect your lives," the weather agency said.
Japan's southern island of Kyushu has seen weeks of heavy winds and rain.
Authorities there had initially issued a level five warning - the highest - and advised more than 800,000 people to leave their homes.
Two people are reported to have been drowned in their cars while another man was swept away while escaping from his trapped car.
"We are seeing unprecedented levels of heavy rains in cities where we issued special warnings," Yasushi Kajiwara of the Japan Meteorological Agency had warned.
Later on Wednesday, the flood warning was downgraded but meteorologists said the danger was not over, and torrential rain may hit the same areas later in the day.
Evacuation orders and advisories are not mandatory yet authorities urge people to heed them and seek safety.
The rain affected the prefectures of Fukuoka, Saga and Nagasaki.
Earlier this summer, Kyushu had already been hit by heavy rain, leading to evacuation advisories for more than one million people.
Last July about 200 people died in western Japan in the country's worst flooding disaster in decades.
It was the highest death toll caused by rainfall in Japan since 1982.