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 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.

Sea Shepherd said "concussion grenades" were also thrown at their activists.

After the day of clashes, Japan's Institute of Cetacean Research announced its work has stopped for the time being.

It said the decision was made because it is too difficult to refuel.

Sea Shepherd founder Paul 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."

Wednesday's clashes follow the sinking of Sea Shepherd vessel the Ady Gil in 2010, which happened as a result of a confrontation with a whaling ship.

Federal Environment Minister Tony Burke earlier said he was trying to confirm the reports.

"Let's wait until I can get those reports confirmed, but I won't be going quiet once I get the information," he said.

But Opposition environment spokesman Greg Hunt says the Government is turning a blind eye to the increasing conflict.

He says he has written to Mr 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."

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.