As powerful typhoon Nanmadol is predicted to hit southwestern Japan, around two million people have been asked to evacuate.
The weather department said that the typhoon could trigger the kind of disaster that is seen only once in a few decades.
Weather officials have issued an emergency warning for violent winds and high waves.
Officials say maximum winds of up to 180 kilometres per hour will lash northern and southern Kyushu, as well as the Amami Islands with peak gusts reaching 252 kilometres per hour.
The agency also warned that as the typhoon is large, rain and winds could intensify even in areas far from it. Heavy precipitation is expected in western and some parts of eastern Japan through Monday.
Meanwhile, Japan Airlines plans to cancel 376 flights. Other airlines are also cancelling services through Monday, mainly on routes serving airports in the Kyushu and Shikoku regions. Bullet train services have also been affected.
Residents in 9,65,000 households have been ordered to evacuate across the seaside cities of Miyazaki, Kagoshima, and Amakusa.
A level five alert, the highest on Japan's disaster warning scale, was issued to more than 14,000 people in the city of Nishinoomote on Kyushu island.