Former Greens leader Bob Brown says the Federal Government must do more to uphold its own whaling laws, after claims a whale was killed in Australia's Antarctic territory.

Dr Brown, who is the head of Sea Shepherd Australia's anti-whaling campaign, says Japanese whalers illegally harpooned a large minke whale near the Davis Research Base on Friday.

The base is inside Australia's Antarctic territory.

Bob Brown resigned as federal Greens leader last year and took up a leading position with Sea Shepherd. ( AAP )

Sea Shepherd founder Paul Watson says the anti-whaling activist group tried to stop the carcass from being transferred from the harpooning ship onto another vessel.

He alleges the whalers attempted to ram their boat - the Bob Barker - but backed off.

The Federal Government is arguing in the International Court of Justice that all Japanese whaling is illegal, regardless of where it occurs, and says there is little more it can do.

But Dr Brown says whaling in Australian waters is illegal and the Government should send naval or customs vessels to assert its laws.

"This Government needs to uphold Australian laws. This Government needs to be doing much more to prevent this illegal, violent, bloody, brutal, nasty slaughter of these whales by this Japanese whaling fleet infringing international law," he said.

Dr Brown says the Government should have sought an injunction to stop Japan's whaling while the case in the International Court is ongoing.

"That's going to go on for many months, that legal action has been taking years. It's not effective in stopping the slaughter of those whales down there at the moment," he said.

Sea Shepherd footage shows Japanese whalers with the carcass of a minke whale. ( YouTube: Sea Shepherd )

'Risk of collision'

Opposition environment spokesman Greg Hunt says the Government needs to send a Customs vessel to the area before the situation escalates.

"We see now that the risk of collision is at extreme levels," he said.

"In freezing waters the risk to life and limb is extraordinary because there are two hostile parties.

"And all the while whales are being slaughtered, this time in Australian waters."

But Environment Minister Tony Burke has rejected the call to send an Australian vessel to the area.

He says the focus should not be just on whether the whale was killed in Australian territorial waters, but on the issue of whaling itself.

"It doesn't matter what part of the ocean it is. In Australia's view, it is just as illegal," he said.

Mr Burke says the correct action to take is what the Government is currently doing in the International Court.

This year the Japanese government has been forced to prop up its whaling program with taxpayer-funded subsidies.

The industry is struggling after several years of militant activists scuttling the catch and a lower demand for whale meat.