A Japanese government spokesman said Tuesday that the death toll from the typhoon has risen to four, with at least 114 injured.
In the wake of a typhoon, the river is flooded.
A man in his 40s was declared dead at a hospital and a man in his 60s was confirmed dead after his car was submerged in floodwater on Kyushu island.
Fourteen people were seriously injured when two more people were found without vital signs.
According to the Japan Times, which spoke to the country, the typhoon made landfall as one of the strongest on record in southern Kyushu island late Sunday night and caused 340,000 homes to lose power on Monday.
The 14th typhoon of the year is considered a category four super typhoon.
The storm dumped a month's worth of rain in a single day as 9 million residents were ordered to evacuate.
The typhoon Hagibis killed 92 people and damaged 85,000 homes. The second most intense typhoon to hit the country in over 70 years was expected to cause billions of dollars in damage from flooding alone. Climate change has been linked to more intense and frequent storms.
The Dominican Republic and Puerto Rico were hit by the first major Atlantic hurricanes of the season. The National Hurricane Center said that the storm had maximum sustained winds of 115 mph.
There are mudslides and flooding in Japan.
Two people are dead as a typhoon hits Japan.
The storm strengthened after hitting Puerto Rico.
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