The Tokyo metropolitan area may see strong winds, though the typhoon is unlikely to pass close to the capital.
Typhoon Jebi, with winds of up to 216 kilometres (135 miles) per hour, swept a tanker anchored in Osaka Bay into a bridge and partially flooded Kansai International Airport on an island in the bay.
Japan's weather agency warned of possible landslides, flooding and violent winds, as well as high tides, lightning and tornadoes in a swathe of the Japanese archipelago.
"Rainstorms will likely intensify suddenly as the typhoon is approaching while picking up speed", the official said, urging people not to go out unless necessary and prepare for evacuation.
It was bearing down on western Japan and set to make landfall on Shikoku, the smallest main island, before raking across the western part of the largest main island, Honshu, and Osaka, the nation's second-largest city, later today.
Railway services were canceled beforehand in the Kinki region, and many retail businesses announced that they would be closed on September 4.
More than 700 flights were canceled, according to Japanese media, while the Shinkansen bullet train services between Tokyo and Hiroshima was also suspended.
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.
A tanker anchored in Osaka Bay was swept into a bridge and Kansai global airport was partially flooded by high waves whipped up by the storm.
As the typhoon lashed Shikoku and the Kii Peninsula, evacuation warnings and advisories were issued in many areas.
More rain might be welcome in other parts of Japan, which has also been sweating through a deadly heat wave.
The Universal Studios Japan theme park, one of Osaka's main tourist draws, was shut down for the entire day.
It has already left tens of thousands without power and authorities have urged people to move to safety.
The recent slump in rupee also has lifted the import cost of crude oil, subsequently raising fuel prices. The price of petrol on Monday was Rs 86.56 per litre while diesel was Rs 75.54 per litre in Mumbai.
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