The 26 people on board included 24 tourists, the captain, and a 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 apparently got into difficulties.
Authorities lost contact with the crew on Saturday afternoon; the crew reported that water was flooding into the stern of the vessel and it had started to sink, Japan’s public broadcaster NHK said.
The crew said the boat was keeling at a 30-degree angle, and those on board were wearing life jackets, NHK reported.
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Authorities believe the vessel sank, but an investigation is still underway.
Patrol boats, aircraft and helicopters are continuing to search for the remaining 16 people who were onboard at the time.
Local media reported waves in the area were up to three meters (9.8 feet) high when the boat issued its distress call.
According to Japan’s Meteorological Agency’s regional website, the temperature of the sea water in the area was a frigid 35 to 37 degrees Fahrenheit (just under 3 degrees Celsius) at the time.