Typhoon Jebi landed with "very strong" force in Tokushima prefecture early afternoon local time, the strongest typhoon to hit the country since 1993, said Akihiro Kikuchi, from Japan's Meteorological Agency.
The typhoon's center made landfall again near Kobe City around 2.00 p.m. local time (1.00 a.m. ET).
Hundreds of domestic flights were canceled, along with international flights from Kansai Airport in Osaka.
Both runways were closed, and later swamped with storm surges that caused record tides in Osaka Bay. Water was also rising near the coastal city of Kobe, Japan's Meteorological Agency said.
Flight cancellations also affected Itami Airport in Osaka and Chubu Centrair International Airport in Nagoya.
Before it made landfall, the storm had sustained winds of 140 km/h (87 mph) and gusts of 165 km/h (102 mph), the equivalent to a Category 1 Atlantic hurricane.
Ahead of the storm two municipalities -- Takamatsu City and Ayagawa Town -- in Kagawa prefecture on the island of Shikoku to the west of Osaka have been hit with evacuation orders as they are at risk of high tides. Tak amatsu is home to over 60,000 residents.
There is a significant threat of widespread flooding. Jebi has dumped over 500 mm of rain in some areas and is likely to produce between 150 and 300 mm of rain in many locations.
Jebi comes just weeks after Typhoon Cimaron, which moved over the same region just weeks ago.
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