Sea Shepherd is claiming victory after Japan temporarily suspended its annual whale hunt in the Southern Ocean.

On Wednesday the anti-whaling group claimed two of its boats, the Steve Irwin and the Bob Barker, were rammed by a Japanese ship in Australian Antarctic waters.

It said the attacks happened after they were ordered to leave the area by one of the boats in the Japanese whaling fleet.

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It also claimed armed Japanese coastguards threw "concussion grenades" at activists on the ships.

Japan's fisheries agency has denied those reports, but confirmed that one of its factory ships, the Nisshin Maru, rammed two boats belonging to Sea Shepherd.

However, it said the clashes happened after activists came too close to a Japanese vessel which was refuelling.

Japan's Institute of Cetacean Research has announced it has stopped work for the time being because it is too difficult to refuel.

Bob Barker captain Peter Hammarstedt has told the ABC that it was the most dangerous confrontation he has ever experienced.

Sorry, this video has expired Sea Shepherd founder Paul Watson speaks to ABC News 24

"The Nisshin Maru collided with my vessel several times and I think we were about 15 to 20 seconds away from being rolled over completely," he said.

Sea Shepherd founder and Steve Irwin captain Paul Watson believes the clashes are a sign of desperation.

"They're losing tens of millions of dollars," he said.

"The world is against them, they know that. Nobody believes for a moment that this is scientific research, it's a commercial operation and so they're being condemned worldwide and I think they're desperate and increasingly more aggressive."

Mr Watson says it is unlikely the whalers will resume their hunt this season.

"Not this season, the season is over in 18 days," he said.

"They couldn't go up north and refuel again. It's all over and done with I think for this year.

"I don't think they have killed more than a dozen whales in total, we don't know for sure, but they couldn't have killed more than that."

Sea Shepherd director and former Greens leader Bob Brown says the confrontation is the worst in the Southern Ocean in three years.

"It's extraordinarily dangerous and it's just a direct breach of international sea laws, international environmental laws, international territorial laws by the Japanese government," he said.

"Tokyo has taken over Australia's territorial waters. It's time the Australian Government reasserted itself. It should send naval vessels down there to reassert international law."

Sorry, this video has expired Whaling suspension not good enough: Burke ( Karina Carvalho )

Opposition environment spokesman Greg Hunt agrees, saying the Federal Government is turning a blind eye to the conflict.

He says he has written to Environment Minister Tony Burke asking for a Customs vessel to be dispatched to the area at once.

"It is time that the Government realises that they are approaching extreme negligence and dispatches a Customs vessel," he said.

"Failure to do so is simply a failure to acknowledge the conflict, the hostility, and the taking of whales in Australian waters.

"Right now there's not just a terrible risk to the whales, but a real risk to life and limb."

However Mr Burke says the Government needs to be wary.

"People need to be very careful to make sure that we don't take action which actually undermines conservation in the Antarctic," he told ABC News Breakfast.

"We are a Government and need to solve and settle this in the court, not the car park."

He says he wants both sides of the conflict to show restraint.

"We always want to see safety at sea, these are reports that are the opposite," he said.

Defence Minister Stephen Smith told ABC News Breakfast this morning that the Government has no plans to send the Navy to the Southern Ocean to monitor the situation.

Australia's Maritime Safety Authority says it is investigating the latest incident.

In 2010 the Sea Shepherd ship Ady Gil sank after being hit by a whaling vessel.

Australia strongly opposes whaling and launched legal action challenging the basis of Japan's so-called "scientific hunt" in December 2010.

Japan claims it conducts vital scientific research using a loophole in an international ban on whaling, but makes no secret of the fact that the animals ultimately end up on dinner plates.