Twenty-one people had been rescued when the search was called off late at night, Melissa Kai, a spokeswoman for the Joint Rescue Coordination Centre (JRCC), said.
A military rescue helicopter and plane had been sent to the waters off the coast of Tofino after the vessel sent a distress signal around 5 p.m. local time, according to the JRCC. Several other coast guard vessels were involved in the search off the rugged west coast of Vancouver Island.
The case had now been turned over to Canadian police as a missing persons case, Kai said.
Eighteen people were taken to Tofino General Hospital, of which three were transferred to other island health facilities, Island Health spokeswoman Val Wilson told Reuters. All were in a stable condition. Some at the Tofino hospital had already been discharged, she said.
Earlier in the evening, military planes and coast guard vessels lit up the area where the vessel remained partially submerged, eight nautical miles northwest of Tofino.
The manager of the Shelter Restaurant in Tofino said fishermen and fishing charter companies had joined the rescue effort, with about 15-20 boats leaving the tourist town.
"Practically anyone who can go will go," said Matthew, who did not give his last name. "People here get together to help when things like this happen."
Tofino, a community of roughly 2,000 people on the west coast of Vancouver Island, is a popular tourist destination for surfers, hikers and whale watchers from around the world.
"All our attention now is on our passengers and crew so we'll be providing information as soon as the time is appropriate," said a staff member with Jamie's Whaling Station and Adventure Centres, which operated the vessel, the Leviathan II.
In 1998, a boat operated by the same company sank near Tofino, killing the ship's captain and a German tourist.
John Forde, who works at another eco-adventure company, said passengers on a vessel like the Leviathan II, a three-deck 65-foot cruiser that can carry up to 46 people, would not have to wear life jackets. The boat, like ferries, would only be required to have life jackets on board.
"The sea was three to four metres, a fairly big sea, but not much wind or too unusual for the conditions we deal with on a regular basis out here," Forde, who took part in the rescue for several hours, told Global television.