Wind gusts of up to 208 km/h were recorded in one part of Shikoku island, with forecasts as high as 216 km/h.
If Jebi maintains its force, it could be the strongest typhoon to hit Japan since 1993.
A powerful typhoon slammed into western Japan on Tuesday, causing heavy rain to flood the region's main global airport and strong winds to blow a tanker into a bridge, disrupting land and air travel and leaving thousands stranded.
Services from Tokyo to Osaka were running reduced operations, while more than 500 flights were cancelled.
Abe had faced criticism over his initial response to heavy rain that pounded western Japan in July, given that he and some other ministers were found to have been drinking at a gathering of the LDP lawmakers in Tokyo as the situation became increasingly grim.
Meanwhile, a 71-year-old man died after being buried underneath a storage unit that collapsed on him.
Public broadcaster NHK said 97 people had been injured across the storm's path, none of them seriously.
In Osaka Bay it swept a tanker into a bridge and in Kyoto parts of the train station roof came down. There were no reports of injuries.
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The country's weather service said it is the strongest typhoon to hit Japan in 25 years.
The terrifying video, shot by the BBC, shows as a lorry is pushed to its side by the hurricane force winds which then rip off an entire side of the vehicle.
Japan issued evacuation advisories for more than a million people and cancelled hundreds of flights as Typhoon Jebi sliced across the west on Tuesday, cutting power, overturning cars and killing at least six people.
Arriving on land, Jebi had winds of up to 162 kilometres (100 miles) per hour at its centre, making it a "very strong" typhoon, the weather agency's chief forecaster Ryuta Kurora told AFP.
Universal Studios Japan, a popular amusement park near Osaka, is closed.
All local train lines run by West Japan Railway Co in the area's three main cities - Osaka, Kobe and Kyoto - remained halted as of 5 pm, as well as all Shinkansen high-speed trains linking Tokyo to Hiroshima.
Typhoon Jebi - whose name means "swallow" in Korean - was briefly a super typhoon and is the latest storm to hit Japan this summer following rains, landslides and floods.
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.
It has already left tens of thousands without power and authorities have urged people to move to safety.