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Sea Shepherd Conservation Society founder Paul Watson said he was aboard the ship Steve Irwin when the Japanese boat Nisshin Maru collided with it, the Bob Barker and a tanker used to refuel the Japanese whaling fleet.
Watson said the Japanese ship deliberately rammed the Sea Shepherd vessels to try to move them aside and get to the refueling tanker. He said the Japanese ship also accidentally hit the tanker. He said the incident, near the Australian Davis Research Base on the Antarctic coast, was particularly dangerous because the tanker was involved.
Japan's Fisheries Agency blamed the Sea Shepherd boats, saying they had taken the offensive and had hit the Nisshin Maru at least four times during refueling despite verbal warnings. No one was injured, but the Nisshin Maru's bow was dented and a handrail was damaged, the agency said in a statement.
"It's unforgivable," the agency said. It said the Sea Shepherd's action was "a dangerous act that threatened the safety of our research fleet and lives of its crewmembers."
Sea Shepherd boats and the Japanese whaling fleet have had past clashes and collisions.
Japan says it hunts whales for scientific purposes, an allowed exception to an international whaling ban, though anti-whaling activists say the hunts are a cover for commercial whaling.
Japan decries Sea Shepherd as a terrorist group that risks lives through tactics used to obstruct the whaling fleet.
Watson said the Bob Barker sustained the most damage in the Sea Shepherd fleet from Wednesday's clash. He said it initially put out a distress call to Australian maritime authorities after it lost power and began taking on water, but that the crew had gotten the situation under control. He said no one from the Sea Shepherd fleet was injured.
Australian Maritime Safety Authority spokeswoman Jo Meehan said they were aware of the reports but weren't involved in any active search-and-rescue operations.
Australian Environment Minister Tony Burke said in a statement that he was seeking more information about the incident.
"The government condemns so-called `scientific' whaling in all waters and we urge everyone in the ocean to observe safety at sea," Burke said.
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