The Sea Shepherd Conservation Society called the boarding of the Farley Mowat "an act of war," Canwest News Service reported.
Paul Watson, the head of the organization, said a communications officer on the vessel called him during the raid.
"While I was talking to her I could hear yelling in the background telling people to lie down on the deck," Watson said. "The crew were forced down at gunpoint and then the line went dead. So they obviously cut the communications."
The operation was carried out by the Royal Canadian Mounted Police and coast guard. The captain and first officer of the Farley Mowat, named after one of Canada's best-known environmentalists, were arrested.
Minister of Fisheries and Oceans Loyala Hearn said the Sea Shepherd group ignored warnings to obey regulations.
"They are a bunch of money-sucking manipulators, and their sole aim is to try to suck as much money out of the pockets of people who really don't know what's going on," he said.
On its Web site, the group describes itself as an international non-profit organization that works to defend wildlife and habitat in the world's oceans.