Jebi has a similar trajectory to Typhoon Cimaron which made landfall on August 23, disrupting transport but causing limited damage and few injuries.
The winds are so strong that they pushed a 292-ft-long tanker ship from its anchored position at sea into a bridge near Osaka.
According to the regional headquarters of the Japan Coast Guard, a tanker smashed into an access bridge to the airport at 1:32 p.m.
After passing the southern part of Tokushima Prefecture, the typhoon passed near Kobe and moved into the Sea of Japan, the Japan Meteorological Agency said.
Japan's weather agency has issued warnings about possible landslides, flooding and violent winds, as well as high tides, lightning and tornadoes in a swath of western Japan including the major cities of Osaka and Kyoto.
High waves hit breakwaters at a port of Aki, Kochi prefecture, Japan, Tuesday, Sept. 4, 2018.
Shinzo Abe, the prime minister, urged people not to wait for mandatory evacuation orders to abandon their homes as Typhoon Jebi, known as Typhoon 21 in Japan, struck the island of Shikoku and the centre and west of the main island of Honshu.
Japan is now in its annual typhoon season, and is regularly struck by major storm systems during the summer and autumn.
Japan has issued evacuation advisories for more than one million people, according to the Reuters news agency.
Wind gusts of up to 166 km/h were recorded in one part of Shikoku, with forecasts for gusts as high as 216km/h.
Video posted on Twitter showed a small part of the roof of Kyoto train station falling to the ground.
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.
Other video showed roofs being torn off houses, transformers on electric poles exploding and a auto scudding on its side across a parking lot.
More than 700 flights were canceled, according to Japanese media tallies.
Hundreds of flights, trains and ferries had to be cancelled.
The storm paralysed the country's second-largest population center around Osaka, with companies forced to temporarily close their plants, and power cut to more than 800,000 homes and offices.
In Osaka, the Universal Studios Japan theme park and U.S. Consulate were both closed.
While Tokyo will be spared the worst of the storm, authorities have warned of very strong winds and heavy rain even in the capital.