The typhoon made landfall Wednesday afternoon near the city of Hamamatsu, about 125 miles (200 kilometers) west of Tokyo, and then cut a path to the northeast and through the capital before bringing new misery to the tsunami zone. It dumped up to 17 inches (42 centimeters) of rain in some areas, triggering landslides and flooding.
By midafternoon Thursday, the system had weakened to a tropical storm and had moved out to sea past Japan's northern island of Hokkaido, which was not hit as hard as the main island of Honshu the day before.
On Wednesday, hundreds of tsunami survivors in government shelters in the Miyagi state town of Onagawa were forced to evacuate for fear of flooding. The storm set off landslides in parts of Miyagi that already were hit by the March disasters. The local government requested the help of defense troops, and dozens of schools canceled classes.
Strong winds snapped power lines in many areas, and officials said more than 200,000 households in central Japan were without electricity.
Overnight in Tokyo, where many rush hour trains were suspended for hours, thousands of commuters got stuck at stations across the sprawling city and stood in long lines for buses and cabs.
Fire department officials reported three people injured in Tokyo, but other than the inconvenience of transportation gridlock and winds that made it difficult to walk around the city, the storm passed through without incident.
Heavy rains prompted floods and caused road damage earlier in dozens of locations in Nagoya and several other cities, the Aichi prefectural government said. More than 200 domestic flights were canceled.
A typhoon that slammed Japan earlier this month left about 90 people dead or missing.