Typhoon Trami has been branded a «very strong» storm by Japan Meteorological Agency (JMA) and has made landfall in the Wakayama Prefecture, around 400miles from Tokyo.
Outer winds of the violent storm have already crashed into parts of the country and the storm officially made landfall just after 12pm BST (8pm local time near Tanabe).
More than 3.7million people have been urged to leave their homes with the typhoon on track to sweep across the country.
At least 66 people have already been injured by the category 2 tropical storm and residents are being urged to stay inside away from the dangerous conditions.
Thousands of flights have been cancelled in Japan as the storm neared and Kansai International Airport in Osaka Bay, south of Kyoto, has closed its runways.
Train operators have also shut down services with the storm expected to bring life-threatening storm surge, winds and heavy rain.
Typhoon Trami is forecast to strengthen as moves over eastern and northern Japan on Monday.
In the live webcam of Kobe, a city located near the Wakayama Prefecture, heavy rain and powerful gusts are seen whipping up the sea at the port.
WATCH TYPHOON TRAMI LIVE WEBCAM BELOW
Anyone outside during the height of the storm can endure bodily harm
AccuWeather Senior Meteorologist Kristina Pydynowski
Typhoon Trami has already ripped through southern Japanese islands ripping trees out of the ground and causing power outages.
Around 300,000 people living in Okinawa and Kagoshima are still believed to be without power after the super-typhoon hit.
Accuweather has already predicted more than 400mm of rain will fall widely across the Japanese mainland.
AccuWeather Senior Meteorologist Kristina Pydynowski said: «Anyone outside during the height of the storm can endure bodily harm or be fatally struck by flying debris.
“Storm surge flooding along the entire southern coast of Japan will further threaten lives and property into Sunday night.”
The latest travel advice updated today on the Foreign and Commonwealth Office website reads: “Typhoon Trami is forecast to affect a wide area of Japan until 2 October bringing excessive rainfall, strong winds and possible disruption of essential services.
“If you’re in affected areas, monitor local news reports and follow the advice of local authorities and emergency services including any evacuation orders.”
Some parts of the country are still recovering from the impact of Typhoon Jebi which stuck the country in late August.
At least 17 people died when Typhoon Jebi struck, and at least $2.3billion (£1.77billion) worth of damage was caused.