The category 2 tropical storm, known as Roke , is expected to head toward the north eastern region which was battered by the tsunami in March.
The southern coastline near Tanabe and Nagoya has already experienced winds of over 100mph (160kph) and heavy rain.
Rescuers in boats have been trying to help people whose homes have been hit by floods and landslides.
In the capital, Tokyo, high winds and rain have knocked out the power to 200,000 homes while local authorities battle to strengthen river banks.
The Japanese government has asked people to follow evacuation orders.
Chief cabinet secretary Osamu Fujimura warned: "We need to be extra vigilant against a potential disaster caused by heavy rains, strong winds and rough seas along a wide area from western to northern Japan."
The typhoon has affected much of Japan's industrial heartland and companies including car manufacturer Toyota have closed down their factories.
Also buffeted by the storm is the Fukushima nuclear power plant - which is at the centre of an ongoing radiation crisis since the earthquake and tsunami devastated the coastline on March 11.
The plant's owner, Tokyo Electric Power Co, has said there was no immediate problems reported at the damaged reactors from the storm.Sky News – 1 hour 41 minutes ago
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