Anti-whaling activists claim Japanese whaling ships circled their protest vessel "like sharks" before ramming it off Antarctica.
Sea Shepherd founder, Captain Paul Watson, said the Japanese harpoon ship rammed the conservationists' ship the Bob Barker and tore a 90cm gash in the hull above the water line.
But a group representing the Japanese fleet says anti-whaling activists are the aggressors in clashes with whaling ships off Antarctica.
The Institute of Cetacean Research says Sea Shepherd protest ship the Bob Barker repeatedly fired a high-power green laser device at its crew and then started launching bottles filled with butyric acid.
The incident happened about 300 kilometres off Cape Darnley, in the Australian Antarctic Territory, about 3pm (AEDT) on Saturday.
No-one was injured in the incident.
Capt Watson said the collision was "entirely intentional" on the part of the Japanese.
"Four Japanese ships circled the Bob Barker like sharks," he told AAP by satellite phone.
"Then one of them, the Yushin Maru 3, did a quick turn and rammed a three-foot gash in the hull.
"Luckily, the waters are calm at the moment and we have a welding crew working to fix it."
The anti-whaling vessel was blocking the slipway of the Nisshin Maru, the Japanese whaling fleet's factory ship, when the collision occurred.
Second major clash this year
This is the second major clash between Japanese whalers and anti-whaling activists this year, after the Ady Gil sank following a collision with a Japanese whaling ship in the Southern Ocean on January 6.
Capt Watson called on the Australian government take action on illegal whaling.
"The Japanese are violating Australian laws on whaling and nothing is being done to stop them," he said.
Yet only a few countries recognise Australia's claim to the area. Japan is not one of them.
Japanese Fisheries Agency official Takashi Mori said officials were trying to confirm details of a reported clash, The Associated Press reported.
Video shot from the Bob Barker and released by Sea Shepherd shows the two ships side by side moving quickly through the water, the AP said.
The ships come closer together and the Japanese ship then appears to turn away, but its stern swings sharply toward the Bob Barker.
The collision is obscured by spray, but a loud clanging noise can be heard before the vessels separate.
Capt Watson said the Yushin Maru 3 appeared to stop moving after the collision and had not been seen by the Bob Barker's crew to have moved since, suggesting it also may have been damaged.
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