Sea Shepherd said one of its vessels, the Bob Barker, was struck during a coordinated attack by the Japanese fleet's three harpoon ships as they attempt to drive the campaigners away from the factory ship Nisshin Maru.
"The Bob Barker was hit by the Japanese whaling fleet's harpoon vessel, the Yushin Maru No 2, as the harpoon vessel crossed in front of the bow of the Sea Shepherd ship," the activist group said.
"The assault is an attempt to deter the Sea Shepherd ships from their current position, blocking the slipway of the Nisshin Maru, preventing the whalers from loading whales poached from the Southern Ocean Whale Sanctuary."
Sea Shepherd said the Japanese had attempted to damage the fleet's propellers with steel cables, had thrown projectiles including grappling hooks at the Steve Irwin and fired water cannon on the Bob Barker's crew as they tried to cut the cables from a small boat.
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Bob Barker captain Peter Hammarstedt said the Sea Shepherd vessels were "unprovokedly attacked" by the Japanese harpooners in a "ruthless" fashion.
"These harpoon ships came in heavy and hard. They hit my bow with about 300 metres of steel cable with the express intent of causing damage to my rudder and propellers," he told the Australian Broadcasting Corporation.
Hammarstedt said nobody was injured "but certainly the whalers were more aggressive than we have ever seen them before and I think we're quite lucky that nobody was hurt."
Hammarstedt said the collision had left his anchor dangling "like a wrecking ball" but most of the damage was above the water line and would be able to be repaired at sea.
High-seas confrontations are common between Sea Shepherd and the Japanese, who hunt whales in Antarctica under a "scientific research" loophole in the moratorium on whaling.
The anti-whaling group, carrying out their 10th annual harassment campaign of the Japanese fleet, said their actions had so far produced a "disastrous" season for the harpooners.
"Early interception and a persistent chase has enabled the Sea Shepherd Fleet to effectively suspend whaling operations and allowed the fleet to take up position and secure the slipway of the Nisshin Maru," it said.