The alleged killing of a whale in Australian waters has led to a dangerous confrontation between Japanese whalers and Sea Shepherd activists.

Sea Shepherd founder Paul Watson says Japanese whalers illegally harpooned a large minke whale near the Davis Research Base yesterday.

The base is inside Australia's Antarctic territory.

Mr Watson says when they tried to stop the carcass from being transferred from the harpooning ship onto another vessel, the whalers attempted to ram their boat.

"I think it was to test our resolve because they thought that we wouldn't block them," he said.

"They came in so close, they tried to ram the Bob Barker so it backed off but I don't think they are going to try that again.

"It's sort of a stand-off. The Steve Irwin's racing to catch up with them and we're being followed by the Nisshin Mauru 3."

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, saying there is little more the Government can do about whaling in Antarctic waters.

He says the Government is arguing in the International Court of Justice that all Japanese whaling is illegal, regardless of where it occurs.

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

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.