Neoguri, which made landfall Thursday morning, reached Futtsu in Chiba prefecture, some 45 kilometres (30 miles) southeast of central Tokyo, shortly before 5:00 am (2000 GMT 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 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 Friday, will move northeast 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 126 kilometres (80 miles) per hour.
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.