Three people have been rescued so far, the Kyodo news agency reported, citing the coast guard.
There were a total of 12 people on board of the ship: three citizens of Myanmar, seven of China and two more of Vietnam.
Japan is currently facing the powerful typhoon of Hagibis, which has already left at least eight people dead, 106 injured and 17 more missing. Millions of Japanese citizens received recommendations to evacuate because of the typhoon.
According to the NHK broadcaster, more than 800 flights have been canceled in Japan over the typhoon. The disaster has also breached the railway traffic.