With maximum wind speeds of 130 miles per hour, the typhoon drenched the western and central part of the country, which also was blasted two weeks earlier by another fierce storm.
The deluge caused fears of landslides and flooding, particularly in Nagoya, the fourth-largest city, located about 170 miles west of Tokyo.
The Associated Press reported that 13 people were dead or missing as a result of the storm.
The typhoon later Wednesday moved into the northeastern coastal region, which is still trying to recover from the March 11 earthquake and tsunami.
At the damaged nuclear plant in the region, Fukushima Daiichi, plant workers took measures to prevent typhoon damage, fixing tarpaulins over buildings to prevent leakage. AP reported that the storm grazed the plant but caused no immediate problems except a broken security camera.
Earlier in the day, the Tokyo Electric Power Co., which operates the plant, said that the makeshift cooling system — installed earlier this summer in an effort to stabilize the reactors — will not be damaged by the typhoon.
The Japan Meteorological Agency called for “the greatest possible vigilance,” advising local authorities to take precautions against landslides. The typhoon, the 15th of the season in Japan, comes just two weeks after Typhoon Talas, which killed 67 and left dozens more injured.
The city of Nagoya temporarily called off an evacuation warning for 880,000 people when swelling in a major river subsided, but officials said the warning could be reissued if conditions warranted.
Heavy rains caused floods and road damage in dozens of locations in Nagoya and several other cities. Police in Gifu prefecture said a 9-year-old boy and an 84-year-old man were missing after apparently falling into swollen rivers, AP reported.
Toyota Motor Corp., Japan’s No. 1 automaker, was shutting plants as a precaution, the wire service said. Machinery maker Mitsubishi Heavy Industries told workers to stay home at its five plants and an office in the Nagoya area.
Nissan Motor Co. spokesman Chris Keeffe said workers at its Yokohama headquarters and nearby technical facilities were being told to go home early for safety reasons, and two plants were not operating, AP said.