Neoguri landed at Chiba prefecture east of Tokyo at around 5 a.m. accompanied by winds that reached up to 126 km an hour, according to the Japanese Meteorological Agency (JMA).
The typhoon has been weakening as it moved north-east and is expected to become an extra-tropical depression after crossing the Boso Peninsula that forms the eastern edge of Tokyo Bay, and reaching the Pacific Ocean.
However, the Japanese capital and other areas in the central part of the country remained on alert Friday due to the forecast of torrential downpour and violent winds.
The operator of the troubled Fukushima Daiichi nuclear power station indicated that it was "fully prepared" for the storm, which however was not expected to hit the plant.
In a statement, Tokyo Electric Power Company Ltd (TEPCO) said it would temporarily suspend the dismantling of the reactor and other work if the rain and wind intensify.
The typhoon has left three people dead and 66 injured in southern and central Japan this week and has caused serious damage to 117 houses.
A 12-year-old boy died after he was swept away in a flood in front of his house only 10 minutes before authorities issued an evacuation warning, national channel NHK reported Thursday.
Two men also drowned in different parts of the country after falling into swollen rivers.
The typhoon has forced the evacuation of 30,000 people on the south-western Kyushu island and temporarily left thousands of homes without power in both that region and Okinawa, where it reached its maximum intensity.