The weather agency warned people across Japan to be on alert for "violent winds, high waves, heavy rain".
Streets in the Okinawa prefectural capital of Naha were deserted Sept 29 as winds and rain from Typhoon No. 24 battered the island. Evacuation orders were issued for tens of thousands of people over a widespread area, including more than 250,000 people in the city of Tokushima on the island of Shikoku, the national broadcaster NHK reported.
Western parts of Japan are still recovering from the most powerful typhoon to strike the country in a quarter of a century, which claimed 11 lives and shut down the main regional airport in early September.
A woman in her 60s went missing in Miyazaki prefecture, southern Japan, after she was washed away in a paddy irrigation channel, according to NHK.
Airlines cancelled or plan to cancel more than 930 flights, public broadcaster NHK said.
The typhoon is expected to move up the country in a north-easterly direction over Sunday and into Monday.
As of noon September 29, the typhoon was about 40 kilometers south-southeast of Okinawa's Kumejima island and moving northward at a speed of 20 kph.
Tokyo Metro announced it will suspend operation of some subway trains from 9 p.m.
Trump's tariffs on $200b of Chinese imports kick in
Some analysts say there is also a risk that China could allow its currency to weaken again to cushion the blow to its exporters. Trade Representative Robert Lighthizer that the new tariffs could result in higher consumer prices at its stores.
The storm cut power to about 200,000 homes on Japan's southern islands, and uprooted tress and overturned vehicles as it pummeled Okinawa city.
Storm surges are forecast to hit coastal areas along the typhoon's route, including the bays of Osaka, Ise and Mikawa in western and central Japan. The terminal building was closed for the day and the monorail as well as bus service to the airport were also suspended.
Photo taken on September 29, 2018, shows waves crashing on the coast of Yonabaru, Okinawa Prefecture, as typhoon Trami approaches Japan's southernmost prefecture.
"We are strongly urging our residents to stay indoors because it is extremely unsafe to be outside now", Masaaki Tamaki, an official of Kagoshima's disaster management section, told AFP.
There have already been heavy downpours in large areas of western and eastern Japan, including the capital, as the storm spurred a seasonal rain front.
Maintaining its "very strong force", the storm churned near Kagoshima on the western tip of Japan, causing seven minor injuries. Some Tokyo train lines stopped running even before 8 p.m. Sunday, with the central Tokyo Yamanote loop line and others halting at 8 p.m., according to notices on the East Japan Railway website.
Also in September, a magnitude 6.6 quake rocked the northern island of Hokkaido, sparking landslides and leaving more than 40 people dead.