Japan's Institute of Cetacean Research is flatly denying it rammed any ships in the Antarctic.

The anti-whaling group Sea Shepherd says one of its vessels, the Bob Barker, has been damaged in a collision in the Southern Ocean whale sanctuary leaving a metre-long gash in its hull. Sea Shepherd claims the Japanese rammed it deliberately, but Institute spokesman Glenn Inwood says the impact was far from deliberate.

"Japan is doing a legal operation there. It has no need to ram anyone. This is all the work of the Sea Shepherd group."

Mr Inwood says the Yushin Maru was trying to avoid acid bombs being lobbed by crew on the Bob Barker and in doing so, the vessel made a dramatic turn, clipping the Bob Barker. He also claims the protesters had been repeatedly firing a high-power green laser device at the Nisshin Maru crew.

Sea Shepherd admits to actively blocking the slipway of the Japanese whaling fleet's factory ship when the collision occurred. It was trying to prevent slaughtered whales being loaded onto the vessel.