The first footage of the annual Antarctic "whale wars" has been released, showing Japanese sailors using high-power water cannons to deter activist boats.

Both sides are already claiming the use of undue force by the other in the first high seas clash between Japanese whalers and conservationist group Sea Shepherd.

The Japanese Government's Institute of Cetacean Research said in a statement its vessel the Yushin Maru 3 had been subjected to a five and half hour attack by crew from the Sea Shepherd's Bob Barker on January 4.

The ICR said the crew had crossed the bows of the Yushin Maru 3 in small rubber boats at least 30 times and had attempted to disable the ships' rudder using wires and tow ropes.

"During the attack the YS3 broadcasted a warning message and made use of its water pump asa preventive measure to make activists desist from further approaching," it said in a statement.

In reply, Sea Shepherd said the whalers had broken one of the boat's radars in the skirmish.

Sea Shepherd leader Paul Watson, who was on his way to Fremantle, said the Bob Barker had come across the Yushin Maru 3 during its search for factory ship Nisshin Maru.

He said the Yushin Maru 3 was using very high powered water cannons that had more force than in previous years.

"They must have spent around three quarters of a million dollars on water cannons for that boat alone," Watson told the West Australian newspaper.

Sea Shepherd says the Bob Barker will continue its search for the Nisshin Maru, which had previously been tracked with the use of a drone launched from on board the Steve Irwin.

The protesters' tactics include trying to blockade the factory ship to stop the whale catch being processed.

The Bob Barker is the only Sea Shepherd ship currently operating after the Brigitte Bardot was forced to return to Western Australia with hull damage caused by a freak wave.

The Steve Irwin had escorted it to Fremantle where it docked last night, while the Japanese government security ship, the Shonan Maru 2, was waiting offshore, the group said.

No whales have yet been killed.

"Because the Nisshin Maru and the harpoon vessels have been moving continuously since first located by Sea Shepherd, they do not appear to have had any time to kill whales," the group’s statement said.

"They know that if they slow down or stop the Bob Barker will close the gap and will be on them."

Sea Shepherd had earlier asked the Australian government to send a ship to observe the activities of both the whalers and protesters.

In return, the ICR called on the Australian government to take action against the Sea Shepherd saying Japan's whaling in the Antarctic "was a perfectly legal activity" carried out under the International Convention for the Regulation of Whaling.

- © Fairfax NZ News