Militant anti-whaling campaigners Sea Shepherd said one of their ships was rammed Sunday during "aggressive" and "unprovoked" confrontations with the Japanese in the Southern Ocean.

Sea Shepherd said one of its vessels, the Bob Barker, was struck during a coordinated attack by the Japanese fleet's three harpoon ships as they tried to drive the campaigners away from the factory ship Nisshin Maru.

"The Bob Barker was hit by the Japanese whaling fleet's harpoon vessel, the Yushin Maru No. 2, as the harpoon vessel crossed in front of the bow of the Sea Shepherd ship," the activist group said.

"The assault is an attempt to deter the Sea Shepherd ships from their current position, blocking the slipway of the Nisshin Maru, preventing the whalers from loading whales poached from the Southern Ocean Whale Sanctuary."

A Japanese fisheries agency official confirmed the collision, but said it was the Yushin Maru No. 3, not No. 2.

He told AFP: "We have confirmed damages to the Yushin Maru No. 3's stern and the outer shell. The activists also threw rope at the Yushin Maru No. 1. The rope is now tangled in the ship's screw."

He denied Sea Shepherd's statement that it was a coordinated attack by the Japanese fleet.

"That is totally unthinkable. They may have taken it as an attack just after the Japanese ships sailing before their eyes. But in all reality, they were the ones who threw the rope at the ship."

No crew members were injured and the Japanese ships were able to sail despite the damage, he said.

High-seas confrontations are common between Sea Shepherd and the Japanese, who hunt whales in Antarctica under a "scientific research" loophole in the moratorium on whaling.

In 2010 a collision resulted in the sinking of Sea Shepherd's speedboat Ady Gil.

The anti-whaling group, carrying out its 10th annual campaign to harass the Japanese fleet, said their actions had so far produced a "disastrous" season for the harpooners.

Sea Shepherd has three ships out this season, the Bob Barker, Steve Irwin and Sam Simon.

The group said the Japanese had attempted to damage the fleet's propellers with steel cables, had thrown projectiles including grappling hooks at the Steve Irwin and fired water cannon on the Bob Barker's crew as they tried to cut the cables from a small boat.

Bob Barker captain Peter Hammarstedt said the Sea Shepherd vessels were "unprovokedly attacked" by the Japanese harpooners in a "ruthless" fashion.

"These harpoon ships came in heavy and hard. They hit my bow with about 300 metres of steel cable with the express intent of causing damage to my rudder and propellers," he told the Australian Broadcasting Corporation.

"Thankfully because of a lot of evasive manoeuvring I was able to avoid being entangled, but on one occasion one of the harpoon ships came so close that they ended up colliding with my vessel."

Hammarstedt said nobody was injured "but certainly the whalers were more aggressive than we have ever seen them before and I think we're quite lucky that nobody was hurt."