Heavy rain and gale-force gusts were lashing a wide swathe of the archipelago, television footage showed, as pedestrians struggled with their umbrellas and scurried for shelter.
Some crops were damaged and a number of buildings affected by the wind.
The Japan Meteorological Agency said Noul, the first typhoon of the season to hit Japan, would work its way northwest towards the main island of Honshu later in the day.
Forecasters warned of gusts up to 180 kilometres (110 miles) per hour and said there was a danger of high waves, thunderstorms, flood and gales in much of the country.
It was expected to be near Tokyo overnight.
The storm killed two people as it scraped over the Philippines’ northeastern tip, according to authorities, who said Monday that the evacuation of coastal villages and volcanic slopes averted a higher toll.
It later skirted the coast of Taiwan, after 1,000 tourists were evacuated from the scenic Green island in the southeast in anticipation of the storm.
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