There had been concerns that Typhoon Roke could pose more problems for the Fukushima Dai-ichi nuclear power plant, which was sent into meltdown by the March 11 earthquake and tsunami, but officials said the plant weathered the storm without major incident.
Hiroki Kawamata, spokesman for plant operator Tokyo Electric Power Co., said several cameras set up to monitor the plant were damaged, but there had been no further leaks of radioactive water or material into the environment.
“We are seeing no problems so far,” he said.
The typhoon had reached the country's northern island of Hokkaido by Thursday morning after weakening overnight, but there were no immediate reports of damage there. The storm was still packing sustained winds of up to 78 mph (126 kph).
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.
Police and local media reported 16 people dead or missing, most swept away by rivers swollen with rains in the southern and central regions. One person died in a landslide in northern Iwate prefecture and two people were swept away in Sendai in the northeast.
Hundreds of tsunami survivors in government shelters in the Miyagi state town of Onagawa were forced to evacuate for fear of flooding.
Strong winds snapped power lines in many areas, and officials said more than 200,000 households in central Japan were without electricity late Wednesday.
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.
“The hotels in the vicinity are all booked up, so I'm waiting for the bullet train to restart,” Hiromu Harada, a 60-year-old businessman, said at Tokyo Station.
Kyodo said 5,000 people stayed overnight inside Shinkansen bullet trains at Tokyo and Shizuoka stations.
Fire department officials reported three people injured in Tokyo. In the trendy shopping district of Shibuya, winds knocked a tree onto a sidewalk, but no one was hurt. Pedestrians struggled to walk straight in powerful winds that made umbrellas useless.
The storm had 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.
A magnitude-5.3 earthquake struck late Wednesday just south of Fukushima in Ibaraki state. Officials said the temblor posed no danger to the Fukushima Dai-ichi plant, and that it did not cause any damage or injuries in the region.
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.
Tokyo: Heavy rains and mudslides from powerful Typhoon Talas killed at least 18 people in Japan as the storm moved northward past the country on Sunday. At least 43 others are missing, local media said. 
Because of the storm's slow speed, the agency warned that heavy rains and strong winds are likely to continue and could lead to flooding and landslides.