Three anti-whaling demonstrators have been injured after Japanese crew members used grappling hooks and bamboo poles against them in a high seas clash, activist group Sea Shepherd said Wednesday.

The Sea Shepherd Conservation Society, which annually shadows and harasses the Japanese whaling fleet, claimed two activists were struck in the shoulder with iron hooks and one was hit twice in the face with a long bamboo pole.

The Yushin Maru No. 2 (YS2) is tailing the Steve Irwin anti-whaling ship in the Southern Ocean and the incident happened about 300 nautical miles north of Mawson Peninsula in Antarctica, according to Sea Shepherd.

"Our small boats were attempting to slow down the Japanese harpoon vessel Yushin Maru No. 2, which is aggressively tailing the Steve Irwin," Captain Paul Watson said on the Sea Shepherd website.

During the incident, he said American Brian Race was jabbed twice in the face with a bamboo pole, receiving lacerations above his right eye and on his nose.

South African Russell Bergh, a cameraman for cable television channel Animal Planet, was struck in the right arm and shoulder with an iron grappling hook, resulting in deep bruising.

Watson said French photographer Guillaume Collet was also hit in the right arm and shoulder by a grappling hook and injured.

Japan's Fisheries Agency disputed the account, accusing the activists of starting the conflict by using ropes to try to disable the ship's rudder and propeller and hurling at least 30 bottles containing paint.

"They hurled iron hooks with ropes several times. They cut ropes and nets in floats attached to YS2 to prevent outsiders from climbing aboard," Fisheries said.

"YS2 gave warnings, by voice and water cannon, to the obstructive activities. It also used bamboo poles to push back the small boats when they tried to cut off ropes attached to floats and nets against trespassers."

The Agency called Sea Shepherd's actions "extremely dangerous acts which threaten the safety of our country's vessel and the life of its crew."

Three whaling ships, led by the 720-tonne Yushin Maru No. 2, were seen leaving the Japanese port of Shimonoseki on December 6 for the annual hunt, with security measures beefed up after clashes in previous years.

Their mission is officially said to be for "scientific research", with the fleet aiming to catch around 900 minke and fin whales, according to a plan submitted by the government to the International Whaling Commission.

Watson said two of the three Japanese harpoon vessels in the area were tailing Sea Shepherd boats as they closed in on their hunting grounds, effectively preventing them from killing whales.

"We are almost at the limit of the eastern boundary of their self-assigned hunting area," Watson said. "We should be getting close."

A second Sea Shepherd vessel, the Bob Barker, is in the area but a third, Brigitte Bardot, was damaged in high seas and forced to return to Australia earlier this month.

The Brigitte Bardot was escorted back to port by the Steve Irwin, with the Shonan Maru No. 2 in close pursuit.

Three activists from the environmental group Forest Rescue Australia boarded the Shonan Maru as it followed the Steve Irwin back out of port off Australia's west coast on January 7, sparking a diplomatic incident.

Japan only agreed to hand the men over after intervention from Canberra, and they were returned to Australia on Monday by a border protection vessel.