Authorities lost contact with the crew of the "Kazu 1" after they reported water was flooding into the stern of the vessel and it had started to sink, NHK said.
The crew also said those on board were wearing life jackets and the boat was keeling at a 30-degree angle, NHK said.
There were 24 passengers, including two children, on board and two crew members, the broadcaster said.
The coast guard received contact from the ship at around 1.15pm on Saturday and had dispatched five patrol boats and two aircraft in the search.
No one answered calls to the office of the company that runs the Kazu 1 sightseeing tours. According to its homepage, the ship holds 65 people. Tours around the Shiretoko area usually last around three hours, according to the tour company.
The boat left the Utoro port around 10am on Saturday, and was expected to return to port by 1pm, NHK said. Waves had been high and fishing boats in the area had returned to the port by mid-morning.
The sightseeing boat had been in the area of the Shiretoko Peninsula, in the northern part of Japan's northernmost island and was believed to have been near the Kashinu Falls, NHK said.Â
