An aerial view shows a flooded runway at Kansai airport, which is built on a man-made island in a bay, after Typhoon Jebi hit the area, in Izumisano, western Japan, in this photo taken by Kyodo September 4, 2018.
Jebi is to follow Typhoon Cimaron, which made landfall on August 23 disrupting transport links, but injuries and damages were limited.
A man in his 70s died apparently after being blown to the ground from his apartment in Osaka prefecture, while a 71-year-old man died when a storage building collapsed on him, officials said. However, it is set to speed up once it makes landfall, minimising the amount of rain that will fall in one place.
"It is hard to say what impact this typhoon will have on economic activity, if the [Kansai] airport remains closed for a long time, this will affect tourism revenues in the region", said Koshu Tokunaga, spokesman for the Kansai Economic Federation.
Meanwhile, thousands of people have been stranded at Kansai International Airport, located on an artificial island in Osaka Bay, after flooding and damage to the bridge leading to the airport.
Before it made landfall, the storm had sustained winds of 140 kilometers per hour (87 mph) and gusts of 165 kmh (102 mph), the equivalent of a Category 1 Atlantic hurricane.
Footage released by Japanese media showed Kansai International Airport, on the western coast of Japan, nearly completely underwater after heavy rain brought by Typhoon Jebi hit the artificial island.
The strongest typhoon to hit Japan's mainland in 25 years smashed a tanker into a bridge, forcing one of the country's largest airports to close and hundreds of flights to be canceled.
The center of Jebi was about 100 km west-northwest of Sado in Niigata prefecture, central Japan, and heading north-northeast, NHK said.
NHK public television said 126 people were injured.
Damaged traffic boards and telecommunication relay poles are seen after they were brought down by strong winds caused by typhoon Jebi in Osaka. More than 135mph of the winds have attacked Japan till now and the Prime Minister of Japan, Shinzo Abe has motivated the people so that they can protect themselves and their lives.
In the storm-hit areas, there are strong winds and rains.
Meanwhile, AirAsia has cancelled 11 flights from Sept 3-6, affecting travels to three cities connected to Osaka - KL, Bangkok in Thailand, and Honolulu in the US. Television footage showed waves pounding the coastline amid warnings that high tides later on Tuesday would coincide with the storm's passage.
Japan is regularly struck by major storms during the summer and autumn.
More than a million homes were left without electricity due to powerful over the last 25 years of Typhoon in Japan, writes Reuters.