Michaelle Jean created the stir Monday in the Nunavut town of Rankin Inlet, Sun Media reported. She assisted an Inuit elder woman slice open the seals and cut the meat before sampling a piece of the heart.
Paul Watson, founder of the Sea Shepherd Conservation Society, said he was disgusted the British monarch's representative would do such a thing.
"I'm extremely embarrassed to be associated with a governor general of my country eating raw seal meat in that manner. It's barbaric," Watson told the news agency. "I wonder what the Queen would think about that."
However, Jean's actions won praise from Inuits and their advocates for recognizing a centuries-old tradition, the report said.
Earlier this year, the European Union voted to ban all seal products from Canada acquired from the annual commercial hunt, but exempted Inuit seal products, the report said.