Typhoon Haishen drew closer to Japan's southern mainland on Sunday (September 6), bringing potentially record rainfall, wind and high tides.
Authorities urged early evacuation for more than 100,000 households in the southern island.
But local media reported that some shelters have stopped accepting evacuees as a precaution against coronavirus.
In a meeting with cabinet ministers, Prime Minister Shinzo Abe asked citizens to stay alert and follow information from local authorities.
The typhoon has cut power to more than 300,000 homes.
At least two injuries have been reported.
Airlines have cancelled more than 500 flights departing from Okinawa and southern Japan.
Bullet train services are also suspended in parts of the country.
The typhoon was forecast to approach the Goto Islands, to the west of Nagasaki, in the early hours Monday local time.
According to Japan's meteorological agency, it will then move to the Korean peninsula, which was hit by another typhoon on Thursday, leaving at least two dead and thousands temporarily without power.