According to the agency, the boat with two crew members and 24 passengers, including two children, left the eastern port of the northern island of Hokkaido despite high waves and strong wind observed in the area.
The distress signal was received at about 16.15 GMT by the coast guard.
A helicopter and patrol vessels were sent to the suspected location, however, after two-hour search, rescuers were unable to locate the vessel, Kyodo reported.