The predicted course of Jebi will bring it close to parts of Japan that were hit by devastating rain and flooding in July.
Local media said more than a million households were left without power by the storm, and evacuation advisories were issued for almost 1.2 million people, though only another 16,000 were under stronger - though still not mandatory - evacuation orders.
Typhoon Jebi gained super-typhoon status last week when wind gusts intensified with maximum sustained winds almost reaching 180mph.
The meteorological agency said in a televised warning the system could trigger violent winds, landslides and flooding in the southern and southwestern parts of the archipelago, as well as high tides, lightning and tornadoes.
More than 680,000 people had been issued evacuation orders or advisories, Asahi reported.
Amid strong winds and storm surges, Kansai International Airport, built on an artificial island nearly directly in the cyclone's path, suffered flooding to its runway and terminal building.
West Japan Railway Co. halted all local services in the area's three main cities, with some subway lines in Osaka also stopped.
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A woman using an umbrella struggles against strong wind and rain caused by Typhoon Jebi, in Tokyo, Japan, September 4, 2018.
"I urge the Japanese people to take action to protect your lives, including preparing and evacuating early", Mr Abe said, as the severe weather forced him to cancel a planned visit to the southwest of...
After hitting western Japan, it is set to speed up further as it passes over the main island of Honshu and into the Sea of Japan, where it will weaken.
He also instructed his cabinet to "take all measures possible".
The Universal Studios Japan theme park, one of Osaka's main tourist draws, will shut down for the entire day.
More than 200 people were killed when Typhoon Prapiroon churned through the country less than two months ago.
It has already left tens of thousands without power and authorities have urged people to move to safety.