Typhoon Neoguri slammed into Japan's southern main island early today, after lashing the Okinawa island chain, with three people killed.
Powerful winds and torrential rains have battered the country.
"It landed near Akune City shortly before 7am today (2200 GMT)," an official at the Japan Meteorological Agency said.
The typhoon's winds slowed somewhat overnight, with the storm packing gusts of up to 126km/hr as it moved east at 25km/hr.
The system is forecast to move further along the Japanese archipelago later in the week after crossing Kyushu.
The government is set to hold a disaster-management meeting tomorrow morning to discuss how to best cope with the storm.
Officials said Neoguri would bring torrential rain and warned of the risk of flooding and landslides.
The storm forced local authorities to advise half a million people to seek shelter in Okinawa earlier in the week.