The alert by the Japan Meteorological Agency (JMA) was issued in Fukuoka, Saga and Nagasaki prefectures in the northwestern region of the island where unprecedented levels of rain was recorded.
The agency warned that the flooding could occur in other prefectures and urged the people to take immediate safety measure.
A man died in the Saga prefecture after his car got dragged and submerged in water. A woman was found dead after her car fell into a ditch, in the same prefecture. Another man died in Fukuoka prefecture even after he escaped from his flooded vehicle, Efe news agency reported.
The authorities issued evacuation orders and advisories for 1.7 million people across the country and some 40 members of Self-Defence Forces were sent to assist in rescue works.
The emergency services received numerous calls from people trapped in their cars.
The torrential rain reached unprecedented levels in Saga, Fukuoka and Nagasaki, resulting in partial disruption of train services and closure of some expressways in the region.
The inundation also forced temporary shutdown of businesses and affected the manufacturing activities of some of the firms, including, automaker Toyota, which announced suspension of a part of its production in Fukuoka after the installations were affected.
( With inputs from IANS )