The powerful Vongfong "super-typhoon" unleashed winds of over 100mph on the Japanese islands of Okinawa and Kyushu, injuring to least 35 people.
Torrential rain and strong winds have toppled trees, flooded streets and cut power to more than 60,000 homes.
Authorities have also told 150,000 people on Kyushu to evacuate. Landslide warnings have been issued and howling gales have knocked out power lines. The bullet train service was also temporarily halted for several hours.
In Okinawa, the storm had cut power to over 17,000 households and injured at least 23 people on Sunday. A man in his twenties lost a finger to a door slammed shut by strong winds, a municipal official told the Japan Times.
There were many more injuries, including a 9-year-old girl who also had a finger caught in a door.
"These are two separate cases, but in both cases they lost one of their fingers as the door closed violently due to the strong winds," a local official said.
Satellite images of Vongfong showed a perfectly formed eye in the midst of a large swirling disc of cloud. It comes just a week after another storm powered through the country, leaving 11 people dead or missing.
Nasa astronaut Reid Wiseman posted a photo of it taken from the International Space Station, seeing the cyclone blanketing the Earth as far as the eye can see.
— Reid Wiseman (@astro_reid) October 9, 2014
"I've seen many from here, but none like this," he wrote of the storm on Twitter, which is the biggest of the year.
Last week's typhoon killed three US airmen who were washed out at sea in Okinawa, home to around half of the 50,000 American troops stationed in Japan.
The US military told service personnel and their families to stay indoors on Sunday until strong winds and the rain subsided. Emergency services are currently out to assess damage, including broken glass and broken power lines.
Japan's Meteorological Agency said the typhoon could reach the Tokyo city area by Tuesday, then gradually lose strength as it travels up the archipelago.