The Meteorological Agency further said that Typhoon Jebi is expected to cross over the Sea of Japan by late Tuesday, drifting further north, and would weaken to an extratropical cyclone by Wednesday morning.
High waves whipped up by the storm also flooded parts of the airport, where all flights were cancelled, and the severe weather caused power outages and travel chaos across much of the country.
More than 680,000 people had been issued evacuation orders or advisories, Asahi reported.
Based on its wind speeds, Jebi was classified as "very strong" by Japan's weather agency.
Tens of thousands of buildings have been left without power, with more than 700 flights cancelled along with scores of train and ferry services.
Bracing for Jebi, domestic airlines have played it safe, canceling a number of local and worldwide flights mainly scheduled to depart and arrive in airports in western and central Japan.
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Thankfully none of the 11 crew members on-board were injured in the incident, according to the local coast guard.
The strong gusts ripped sheeting from rooftops, toppled trucks on bridges and swept a tanker anchored in Osaka bay into a nearby bridge running to the Kansai International Airport.
He said Jebi may be extremely powerful when it makes landfall.
In Nishinomiya, a Hyogo Prefecture city near Kobe, more than 100 cars caught fire after waves inundated a yard for a vehicle auctioneer, according to the local fire department.
The capital, Tokyo, will be far from the centre of the storm but was set for heavy rains and high winds by the end of today. Shinkansen bullet train services between Tokyo and Okayama were suspended and Universal Studios Japan, a popular amusement park near Osaka, was closed.
Kyodo News reported Honda Motor Company halted operations at its Suzuka plant in Mie prefecture on Tuesday.
The agency warned residents to be on high alert for heavy rain, violent winds, high waves, landslides, inundation of lowland areas and river swelling.