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 after being buried underneath a storage house that collapsed on him, officials said.
As of Tuesday morning ET, the storm still had sustained winds of more than 75 miles per hour and was classified as a strong storm, but over the course of the next day it is expected to weaken significantly.
On Wednesday, boats began ferrying people out of the airport, and buses began to run on one side of the damaged bridge after safety inspections.
According to the disaster management agency, the evacuation advisories were allotted 1.19 million people in central and western Japan.
The storm made landfall on Shikoku, the smallest main island, around noon.
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On Japan's main island of Honshu, nine cities and towns issued compulsory evacuation orders.
Singapore Airlines said it has cancelled four flights: SQ622 and SQ618 from Singapore to Osaka; and SQ623 and SQ619 from Osaka to Singapore.
Damaged traffic boards and telecommunication relay poles are seen after they were brought down by strong winds caused by typhoon Jebi in Osaka on September 4, 2018.
Typhon Jebi - whose name means "swallow" in Korean - is the latest harsh weather to hit Japan this summer following rains, landslides, floods and record-breaking heat.
Almost 600 flights were cancelled, including several global flights departing and arriving at Nagoya and Osaka, along with ferries connecting ports in western Japan.
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Elsewhere, the winds whipped away part of the ceiling from Kyoto station and peeled off multi-storey scaffolding on a building in Osaka.
"I urge the Japanese people to take action to protect your lives, including preparing and evacuating early", Mr Abe said.
An officials of JMA was quoted as saying that the typhoon has been categorized as "very strong" and based on the strength of its top winds, would be the strongest typhoon to make landfall in Japan since 1993. Shinkansen bullet train services between Tokyo and Okayama were also suspended. Television footage showed waves pounding the coastline amid warnings that high tides later on Tuesday would coincide with the storm's passage.
A major airport that was cut off when a huge typhoon smashed through its sole access road was being evacuated Wednesday, as Japan grappled with devastation caused by its most powerful storm in a quarter of a century.
Up to 2.4 million homes and buildings were left without power due to the typhoon, although by early Wednesday the flow had been restored in more than half of them.
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A vessel, rear, tilts on one side as it ran ashore at a pier as a typhoon approached Yonabaru, Okinawa prefecture, southern Japan. In July, heavy rain in western Japan killed 221 people, setting off landslides and flooding.