The victims included seven men and three women, some found unconscious in the water and others washed ashore, the Japan Coast Guard regional office told CNN.
The 26 people on board included 24 tourists, the captain and one crew member. Two of the passengers are children.
The boat, Kazu 1, was on a sightseeing tour around the scenic Shiretoko Peninsula on Japan’s northernmost main island of Hokkaido when it appeared to run into trouble.
The authorities lost contact with the crew on Saturday afternoon; The crew reported that water was pouring into the ship’s stern and it began to sink, Japan’s public broadcaster NHK said.
The crew said the boat was keeled at a 30-degree angle and those on board were wearing life jackets, NHK reported.
Authorities believe the ship has sunk, but an investigation is still ongoing.
Patrol boats, planes and helicopters continue to search for the remaining 16 people who were on board at the time.
Local media reported that waves in the area were up to ten feet high when the boat made its distress call.
Seawater temperatures in the region at the time were a chilly 35 to 37 degrees Fahrenheit (just under 3 degrees Celsius), according to the Japan Meteorological Agency’s regional website.