At least one person has died and at least 170 homes in the coastal city of Oita have burned down or been damaged.
Remains found by a person are believed to belong to a man in his 70s who is missing.
More than 200 firefighters responded in the initial stages and the fire was still under control after 20 hours. The Japanese military has sent helicopters to assist.
The fire started on Tuesday evening and spread quickly with strong winds, among villas and even into a forest. Authorities do not yet know what caused it.
A woman living in the area told the Kyodo news agency that she had to flee at short notice, without her belongings, as the fire "spread like an instant."
Oita is located on the northeast coast of the island of Kyushu, south of Japan's main island of Honshu.
