Typhoon Neoguri brought wind and waves to the Tokyo region early on Friday after causing havoc across small communities in western and central Japan earlier in the week.
Neoguri, which made landfall on Thursday morning, reached Futtsu in Chiba prefecture, about 45km south-east of central Tokyo, shortly before 5am (20h00 GMT on Thursday), the Japan Meteorological Agency said.
Television footage showed high waves slamming into the breakwater in Chiba, while emergency officials hurriedly built temporary barriers against further landslides.
But the impact of the typhoon on traffic in the capital appeared limited early on Friday, with train and flight services scheduled to run as normal during the morning rush hour, local media reported.
Neoguri, which is forecast to be downgraded to a tropical storm later on Friday, will move north-east over the Pacific coastline before gradually leaving the Japanese archipelago, the weather agency said.
The storm's winds slowed overnight, with gusts of up to 126km/h.
More than 680 houses in several prefectures were flooded or damaged due to the typhoon and heavy rain, according to the disaster management agency, with about 489 000 households urged to seek shelter.
Officials said there was still a risk of flooding and landslides as powerful winds and torrential rains batter the country. Local authorities urged half a million people to seek shelter in Okinawa earlier in the week.
More than 60 people have been injured in the wake of the storm, officials and reports said, while as many as five deaths have been directly or indirectly linked to the typhoon.
Neoguri is likely to reach areas near the tsunami-crippled Fukushima nuclear power plant on Friday morning.
The storm's heavy rains may present an extra headache for the plant's operators, with workers already locked in a daily struggle to contain huge amounts of contaminated water - used to keep the destroyed reactors cool - and prevent tainted groundwater from leaking into the sea. - Sapa-AFP