Typhoon Shanshan clipped Japan's eastern coast on Thursday morning, sparing Tokyo but bringing heavy rain, strong winds and high waves to some areas along the Pacific coast.
The fierce storm system was expected to begin moving away from land after brushing Japan's main island, the country's meteorological agency said.
But authorities urged residents to stay on alert as the slow-moving typhoon could still trigger landslides and flooding.
Shanshan was around 150 kilometres (90 miles) northeast of Tokyo off the coast of Mito City at 0100 GMT, the meteorological agency said.
Four people have been injured by the storm, but there have been no reports of major damage, the disaster management agency said.
More than 2,000 people evacuated their homes by early Thursday, with Shanshan still packing gusts of up to 180 kilometres per hour (112 mph).
Its approach towards the greater Tokyo area on Wednesday sparked fears the busy morning commute in the capital could be disrupted on Thursday.
But the worst of the storm's weather had subsided in Tokyo by the morning, leaving behind clouds without major rain and winds.
The typhoon is the latest weather front to batter Japan, which has been sweating through a deadly record heatwave that claimed 124 lives last month.
Heavy rain also devastated central and western parts of the country in July, causing flooding and landslides that killed more than 200 people.