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Paul Watson, Sea Shepherd's founder, vowed to continue to confront the whaling fleet.
Barker, a longtime animal rights advocate, said news of the clash came as a shock.
"To think I had just become involved in it, then they had the worst accident that they've had. I thought, 'Barker, what have you brought onto these people?'" he said.
He said he steadfastly supports Sea Shepherd and was grateful that his namesake ship was able to help.
"I knew that they get in there and try to get between the whalers and the whales," said Barker, 86.
Watson and Barker met through a fellow activist.
"He said he thought he could put the Japanese whaling fleet out of business if he had $5 million," Barker said earlier. "I said, 'I think you do have the skills to do that, and I have $5 million, so let's get it on,' so that's what we did."
Both sides involved in Wednesday's incident gave conflicting versions of what happened.
Sea Shepherd said the Shonan Maru deliberately rammed the 78-foot (24-meter) Ady Gil as it sat idle in the water near Commonwealth Bay. Representatives of Japan's Institute of Cetacean Research, which oversees the whaling fleet, said the activists caused the incident when the carbon fiber and Kevlar trimaran veered into the Shonan Maru's path.
The whaling institute said the Ady Gil came "within collision distance" of another ship on Wednesday, the Nisshin Maru, and repeatedly dangled a rope that could have entangled the ship's rudder and propeller. The Ady Gil's crew lobbed small projectiles designed to release a foul smell, and the whalers responded by firing high-powered hoses to keep the Sea Shepherd vessels away, the institute said in a statement.