The storm was heading northeast toward the Tokai region in central Japan at a speed of 35 kilometres per hour, packing winds of up to 216 kilometres per hour.
It will likely reach Fukushima prefecture, which was severely hit by the March 11 earthquake, tsunami and ensuing nuclear disaster, about 9pm, according to the agency.
The city of Nagoya, a regional commercial hub located near the home of Toyota Motor, issued an evacuation advisory to some 1.09 million residents at one point on Tuesday because of worries that rivers might burst their banks.
The advisory was lifted from parts of the city, but landslide, flooding and tornado warnings affected more than a million people were still in place as night fell.