Japanese whalers deny Sea Shepherd allegations that grappling hooks were thrown at protesters at high sea, saying the claim is a "fabrication" and "manipulation".
Sea Shepherd says three anti-whaling protesters in the Southern Ocean have been injured in the activists' most violent clash with Japanese hunters this season.
Sea Shepherd leader Paul Watson said a small inflatable boat carrying four people had a pontoon punctured by 12-inch grappling hooks thrown by Japanese whalers at 4am (AEDT) today.
"The hooks were very heavy and in fact ripped the seats and damaged some of the A-frames on the inflatables," Mr Watson told AAP via satellite phone from the Southern Ocean.
"If they had caught into people's clothing or into their skin, it would have pulled them overboard into the water," he said.
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Sea Shepherd said Animal Planet cameraman Russell Bergh, from South Africa, and French photographer Guillaume Collet suffered deep bruising from the grappling hooks.
Mr Watson said it was the most aggressive clash with the whalers this hunting season and occurred as his boats tried to close in on the Japanese whalers' main factory ship.
But a spokesman for Japan's Institute of Cetacean Research (ICR) said claims grappling hooks were thrown at protesters were "a fabrication and manipulation".
He said whalers used a long rope with a hook on it to grab ropes the Sea Shepherd activists deployed in an attempt to foul the propellers of Japanese whaling ships.
"If their inflatable got too close while the Japanese crew were retrieving the ropes they use to entangle the props, there is the possibility they could get hurt," the ICR spokesman said.
"Remaining a safe distance from the Japanese vessels to protest peacefully would prevent anyone from getting hurt on both sides," he added.
In a separate statement, the ICR said Sea Shepherd had deployed six ropes and wires just in front of the ship's bow and activists had cut through protective floats and nets around the vessel. It said 30 glass bottles containing paint were also flung at the Japanese crew.
The organisation called on Australia to take every measure to restrain and deal with Sea Shepherd's "criminal actions" in an objective way, in accordance with international and domestic obligations.
Although a worldwide ban on whaling has been in place since 1986, Japan exploits a loophole that allows whaling for scientific purposes.
