Typhoon Jebi, the most powerful storm to hit the island nation in 25 years, also injured at least 300 people, according to officials.
Jebi left at least 3,000 people stranded at Kansai airport, an artificial island located in Osaka Bay in the west of the country.
Authorities said they would start evacuating those stuck at Kansai airport on Wednesday to nearby Kobe airport using high-speed boats and buses.
As a result of the typhoon, more than 1.2 million people were without power. Other essential infrastructures such as train lines were also affected by the storm.
“The government will continue to do everything possible to tackle these issues with utmost urgency,” Chief Cabinet Secretary Yoshihide Suga said in a response to the emergency.
Depending on the damage, it could take up to a week before Kansai airport will be reopened again.
Jebi is considered a category-3 typhoon, out of five on the Saffir-Simpson scale. For a brief moment, it was considered a “super typhoon” because of its power.
Wind gusts of up to 208km/h were recorded in one part of Shikoku, with forecasts as high as 216km/h.
Tides in some areas were the highest since a typhoon in 1961, Japanese public broadcaster NHK said.
Prime Minister Shinzo Abe, who was criticised for the government’s slow response to the natural disaster, cancelled a scheduled trip to Kyushu, Japan’s southernmost main island, to oversee the government’s response to the typhoon.
Damages are expected to put a further strain on Japan’s recovery budget as the country continues dealing with natural disasters.
The threat of further floods comes soon after parts of Japan were hit by torrential rains in July, killing more than 100 people.