Anti-whaling activist group Sea Shepherd claims two of its boats have been rammed by a Japanese ship in Australian Antarctic waters.

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

They say the factory ship, the Nisshin Maru, repeatedly rammed the Steve Irwin and then the Bob Barker, pushing it into a Korean re-fuelling boat.

Sea Shepherd says "concussion grenades" have also been thrown at their activists.

The group's director, Doctor Bob Brown, says he has alerted authorities and wants immediate action against what he calls "multiple breaches of international law".

"I have informed the Government," he told ABC24. "Theses are Australian territorial waters and it is time for the Government to reassert itself and send naval vessels.

"This is the worse incident we've seen since the sinking of one of our vessels.

"It's extraordinarily dangerous and a direct break of the law. The escort vessel hurling grenades is labelled 'Government of Japan'.

"It's flagrantly asserting that they're in control of those waters. Canberra needs to tell Tokyo to hold off immediately."

This incident follows the sinking of Sea Shepherd vessel, the Ady Gil, in 2010 which happened as a result of a confrontation with a whaling ship.

Paul Watson, captain of the Steve Irwin, told the ABC: "They literally ran over the top of the Bob Barker. It looked like a tank crushing a car.

"The bow of the Nishin Maru was towering above the wheel house of the Bob barker. It knocked down their mast and buckled their decks."

Spokesman for Sea Shepherd, Jeff Hansen, says the conflict is escalating.

No injuries have been reported but Mr Hansen added: "We're now under attack, with concussion grenades being thrown in Australian waters at our crew.

"The Nisshin Maru has committed the maritime equivalent of a hit-and-run accident."

Federal Environment Minister Tony Burke says he is 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.

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.

An official at the whaling division of the Japanese government's Fisheries Agency said it was checking the allegations.

Rammed: Japanese whaling ship the Nisshin Maru (back R) as it collides with the Sea Shepherd ship Steve Irwin (front L) ( AFP )

ABC/AFP