The typhoon is the latest weather front to batter Japan, which has been sweating through a record and deadly heatwave, and devastating heavy rain in central and western parts of the country in July
A powerful typhoon was churning towards Japan on Wednesday, prompting the weather agency to warn of heavy rain and strong winds and forcing airlines to cancel scores of flights.
Typhoon Shanshan was expected to be less than 150km from Tokyo around midnight on Wednesday (1500 GMT), sparking fears the busy morning commute in the capital could be disrupted the following day.
The typhoon is coming "very close to the Pacific coast" of eastern Japan, centring on Tokyo, and is expected to move towards northern provinces from late Wednesday and early Thursday, the meteorological agency said.
"There are also risks that it may make landfall," it said, warning it could dump 350mm of rain over the greater Tokyo region over the 24 hours by Thursday noon.
"Please be fully on alert against mudslides, flooding in low-lying areas, flooding of rivers, violent winds, high waves and high tides," the agency said in a statement, urging residents to obey any evacuation instructions.
In the Chiba region east of Tokyo, local officials issued their lowest-level evacuation warning for some residents and urged others to be on stand-by for evacuation orders.
The slow-moving storm is packing maximum gusts of 180kmph and was estimated to be 250km southeast of Tokyo at 0600 GMT on Wednesday.
With rain and winds expected to intensify later in the day, television networks urged Tokyo workers to go home early.
Airlines have cancelled scores of domestic and international flights to and from Tokyo's Haneda airport and the main Narita Airport east of the capital.
The ANA group scrapped 36 domestic flights as well as international flights from Narita to Shanghai and Hong Kong.
The typhoon is the latest weather front to batter Japan, which has been sweating through a record and deadly heatwave. This followed devastating heavy rain in central and western parts of the country in July.
The record rains caused flooding and landslides that killed over 200 people and devastated swathes of the country.