The typhoon first made landfall in the southern part of Tokushima Prefecture at 12 pm (local time), before striking for the second time near Kobe city at around 2 pm (local time), The Japan Times reported.
Two people already died and several have been injured during the violent winds.
A tanker anchored in Osaka Bay was swept into a bridge and Kansai worldwide airport was partially flooded by high waves whipped up by the storm.
Prime Minister Shinzo Abe, who has been traveling across the in a bid to bolster his support ahead of the ruling Liberal Democratic Party's leadership election later this month, canceled his trip to the Kyushu region to deal with the typhoon.
The meteorological agency said Jebi was expected to pass over the Sea of Japan by late Tuesday and to have weakened to an extratropical cyclone by Wednesday morning.
ANA Holdings Inc. and Japan Airlines Co cancelled a total of 585 domestic and 13 worldwide flights, and Prime Minister Shinzo Abe cancelled a planned trip to Fukuoka in the southern island of Kyushu to deal with the disaster response.
All Nippon Airways Co. and Japan Airlines Co. have canceled 309 and 264 flights, respectively.
He also instructed his cabinet to "take all measures possible".
One-million people have been advised to leave their homes in Japan to escape Typhoon Jebi, the country's strongest typhoon in 25 years, which has caused at least six deaths and 160 injuries.
Television footage showed waves pounding the coastline, sheet metal tumbling across a parking lot, cars turned on their sides, dozens of used cars on fire at an exhibition area, and a big Ferris wheel spinning around in the strong wind.
The country has been bracing for flooding as the strongest typhoon to hit the country in 25 years tears through parts of the west of Japan.
More than 700 flights have been cancelled, according to Japanese media tallies.
Japan is regularly struck by major storms during the summer and autumn. Shinkansen bullet train services between Tokyo and Hiroshima were suspended and Universal Studios Japan, a popular amusement park near Osaka, was closed.
The country has been sweating through a record, deadly heatwave that was preceded by record rainfall in parts of western and central Japan that killed over 200 people.
Officials ordered more than a million people in affected areas to evacuate their homes amid warnings of high waves, flooding and mudslides.
Since the disaster, authorities have urged people to take evacuation warnings more seriously and prepare to evacuate immediately when the warnings are issued.