The endangered orca, known as J-32, was reported floating in the water near Courtenay on Thursday. The area is located on the eastern side of Vancouver Island more than 200 kilometres northwest of Victoria.
Officials with the Department of Fisheries and Oceans moved the carcass to a boat launch Friday evening, where it was set to undergo a post-mortem examination on Saturday.
By morning, several teeth were damaged or removed, said Paul Cottrell, the Pacific marine mammals co-ordinator for the Department of Fisheries and Oceans.
"Her jaw and teeth were in great shape and solid," Cottrell said in an interview Sunday.
"It looks like they broke off a couple, and there were a number that were sawed off, and those were cut off right to the gum."
Cottrell said fisheries officers are following up on a number of leads.
He said the department doesn't know what motivated the theft, such as whether it might be linked to the sale or trade of endangered species.
The federal Species At Risk act makes it illegal to possess part of an endangered or threatened animal.
The law carries a range of sentences depending on whether the perpetrator is a corporation, non-profit group or a private citizen. For individuals, the maximum penalty is a fine of $250,000, up to five years in prison or both, though maximum sentences are rarely imposed.
"It's just a senseless, illegal act," said Cottrell. "We take this kind of thing seriously. We don't want endangered species parts being traded or sold."
Biologists who have been examining the whale have yet to determine a cause of death.
The necropsy revealed the whale was pregnant with a full-term fetus.
Marcie Callewaert of the Victoria Marine Science Association, a fledging group that she hopes to turn into a non-profit soon, said she went to the area to see the whale on Saturday.
Callewaert said it's significant any time an orca dies, and she said the missing teeth just makes it worse.
"I set eyes on her on the beach about the same time a lady told me that her teeth had been cut the night before, so that was two blows at once," said Callewaert, a Grade 6 teacher who spends her summers as a whale-watching photographer.
Tissue samples from the orca and the fetus will be examined at a number of labs across North America, said Cottrell of Fisheries and Oceans Canada. Results are expected in four to six weeks.
The skeletons will be donated to the Royal B.C. Museum.
The death of the orca is considered a significant blow to the killer whale population and efforts to rebuild it.
J-32 was a southern resident orca. Until the animal's death, there were believed to be 78 southern residents in the wild. Of those, 17 to 18 were believed to be reproductive females.
"When you have 78 animals and you lose an animal that is just going into breeding age — a female that has the potential to contribute for decades — that's a huge loss to this population," said Cottrell.
"Just the fact that she was so close to giving birth, it's unfortunate, because that calf, if it had lived, would be significant to the population."
Cottrell credited the Marine Mammal Response Program, a network of volunteers along the coast who report injured or dead animals, for alerting the department to the orca so quickly, allowing biologists to retrieve a "pristine" specimen for examination.
"If we didn't have the program, we wouldn't have been able to secure and get this animal and be able to necropsy such a fresh animal," he said.