Typhoon Trami, packing gusts of a maximum 162 kilometres (100 miles) per hour near its centre, was in the Pacific spiralling slowly towards Japan's southern islands.
"As it is forecast to go across Japan at a high speed, we are urging people to be vigilant" in the days ahead, Sakiko Nishioka from the meteorological agency told AFP.
The typhoon was now moving northwest slowly but was expected to turn eastward, coming very close to the islands of Okinawa and Amami on Saturday, the agency said in a statement.
"Please be on high alert against violent winds, high waves and heavy rainfall," it said.
After dumping torrential rain on the outlying islands, the typhoon is forecast to pick up speed and approach western Japan on Sunday, remaining very strong as it barrels over the mainland.
Images from the International Space Station posted on Twitter by astronaut Alexander Gerst on Tuesday showed Trami's enormous eye which he said was "as if somebody pulled the planet's gigantic plug".
Japan's main two airlines JAL and ANA have already started to cancel some domestic flights, scrapping more than 100 between them to the islands.
If the forecast holds, it will be the latest in a series of extreme natural events to strike Japan.
Western parts of Japan are still recovering from the most powerful typhoon to strike the country in a quarter of a century, that claimed 11 lives and shut down the main regional airport in early September.
Deadly record rains also hit western Japan earlier this year and the country sweltered through one of the hottest summers on record.
Also in September, a magnitude 6.6 earthquake rocked the northern island of Hokkaido, sparking landslides and leaving more than 40 people dead.
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