The anti-whaling group Sea Shepherd says one of its boats has been hit by a Japanese vessel in the Southern Ocean.

The group says the Ady Gil was at a standstill in Australian waters off Commonwealth Bay when the Japanese whaling ship Shonan Maru 2 deliberately rammed into it.

Sea Shepherd spokesman Chris Aultman, a helicopter pilot for the group, says no crew members were injured in the incident, but the ship has been destroyed.

"The vessel was dead in the water. It was completely and absolutely a wilful act," he said.

"Luckily no one was in the bow of the vessel at the time of the collision or they certainly would have been killed instantly."

Lacky Maclean, the first mate of the Sea Shepherd's ship, the Steve Irwin, says the bow of the Ady Gil was cut off in the attack.

"There's a big difference between throwing stink bombs and sinking a vessel," he said.

A spokesman for Japan's Fisheries Agency, which oversees the country's whaling program, says it is investigating the incident.

The Federal Government has repeated its call for restraint by all parties in the Southern Ocean.

Earlier in the day the Ady Gil clashed with a different Japanese whaling boat.

Sea Shepherd unveiled the Ady Gil in October last year, describing it as "a fast, futuristic-looking trimaran that recently set the world record for global circumnavigation".

The ship, which can reach up to 50 knots, was used to intercept and block harpoon ships from killing whales.

Captain Paul Watson, the president and founder of Sea Shepherd, had said the ship enabled the group's current campaign to be the "most ambitious and aggressive effort to date".