Japan's weather agency has warned of possible landslides, flooding and violent winds, as well as high tides, lightning and tornadoes in the areas affected.
He instructed his cabinet to "take all measures possible". Jebi is predicted to bring heavy rains tomorrow.
Dramatic footage on social shows the roofs being blown off buildings and a truck being knocked over in the strong winds.
A drastic rise in the sea level and tides that may reach record heights could hit the coasts of Osaka Prefecture and southern Hyogo Prefecture on September 4, the JMA said.
Another man in his 60s fell two metres into a rice paddy field in Mima city, the report said.
ANA Holdings said it was cancelling 247 domestic and 8 global flights, while Japan Airlines pulled 176 domestic flights.
The storm has paralysed Japan's second-largest population centre, with flights and trains cancelled across the region and factories forced to temporarily close.
Tomonori Kawaguchi, a 63-year-old company employee who lives in Suita, Osaka Prefecture, who was on his way to his office said he planned to "head home earlier".
An aerial view shows a flooded runway at Kansai airport, which is built on a man-made island in a bay, after Typhoon Jebi hit the area.
Universal Studios Japan, a popular amusement park near Osaka, is closed.
West Japan Railway Co. has begun halting local trains and plans to stop all local services in the area's three main cities. A spokeswoman for the airport said it doesn't know when it can resume operations.
Some parts are likely to see up to 300mm of rain fall in a 24 hour period with winds gusting up to 216 kilometres per hour.
The agency's chief forecaster, Ryuta Kurora, told a news conference on Monday that Typhoon Jebi is stronger than the storm that struck western Japan last month.
The after-effects of the storm are unlikely to be felt in Tokyo.