Typhoon Roke is on course to hit Fukushima, where engineers are still struggling to bring a nuclear plant under control after the March tsunami.
There are concerns that rain could force radioactive water into the sea.
Across Japan more than a million people were urged to evacuate their homes; an advisory was later lifted in one area but 330,000 people remain at risk.
The typhoon made landfall on Wednesday afternoon (0500GMT), scouring its way up the main island of Honshu, bringing high winds and torrential rain.
The storm is tracking a path across Tokyo towards Fukushima prefecture and is then expected to travel up along the north-east coast, which was battered by the 11 March earthquake and tsunami.
Tokyo says pools of radioactive water remain at the Fukushima nuclear site, and there is concern that a heavy downpour could cause them to overflow into the sea or groundwater.
Four people have been found dead after heavy rain and flooding in central and western Japan due to the storm's approach.
Two people are missing in the central prefecture of Gifu, including a nine-year-old boy.
Several motorways have been closed and hundreds of flights cancelled. Car maker Toyota is suspending production at 11 of its 15 factories.
Japan's Meteorological Agency has urged "the highest level of caution be used because of the heavy rain, strong wind, and high waves."
The agency has warned of downpours over a wide area of the country on Wednesday, saying some places could be deluged by as much as 50mm of rain in an hour.
This is the second time in less than a month that Japan is being lashed by a typhoon. Talas ripped through the west of the country, leaving about 90 people dead or missing.
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