The Japanese Meteorological Agency on Saturday warned of “unprecedented” risks of an “extremely dangerous” storm moving towards the island of Kyushu, south of the archipelago.
He urged residents to take shelter before the route to Nanmadol, which was traveling at a speed of 270 km/h, on Saturday.
The typhoon is classified as a “severe” hurricane, the agency’s highest level.
It should head to the main island of the archipelago on Sunday, in Kagoshima Prefecture, south of Kyushu Island, before turning north on Tuesday.
“There is a risk of unprecedented storms, high waves, floods and record rainfall,” Ryuta Kurora, head of forecasting service at the Japan Meteorological Agency, told reporters.
“We must take maximum precautions,” he said, calling on residents to evacuate quickly because “this is a very dangerous typhoon”.
Mr Kurora said the weather agency could issue a maximum alert for the Kagoshima area on Saturday.
This will be the first typhoon-related special alert issued outside the Okinawa region since the system was installed in 2013.
“The wind will be so strong that some houses may collapse,” Kurora said, warning of floods and landslides.
An evacuation “order” – level four on a scale of five – has been issued for the 330,000 residents of Kagoshima city, and officials urged people to move to shelters.
In Japan, evacuation alerts are not mandatory, and during past extreme weather events, officials have sometimes struggled to persuade residents to seek shelter as soon as possible.
Japan is currently in the midst of a typhoon. It is affected by about twenty such storms per year.
According to the websites of Japan Airlines and All Nippon Airways, before the storm hit, flight cancellations began affecting regional airports including Kagoshima, Miyazaki and Kumamoto.