THE federal government says whaling by Japan is illegal wherever it happens, after a large whale was harpooned in Australian waters.

Anti-whaling activists at Sea Shepherd said Japanese whalers killed a large minke whale on Friday in Australian waters off Antarctica near the Davis Research Base.

The group has posted photos of the incident online.

Sea Shepherd founder Paul Watson said when the protesters tried to block the transfer of the harpooned whale's carcass from one vessel to another, the irate whalers tried to ram their boat.

Environment Minister Tony Burke said the focus should not be on which part of the ocean this happened.

"It doesn't matter what part of the ocean it is in, Australia's view is that it is just as illegal," Mr Burke told reporters.

"That's why we have taken Japan to the International Court of Justice.

"I think it would be a terrible situation if we started to go down the path of arguing that in one part of the ocean we thought whaling was okay and in others it wasn't."

Coalition environment spokesman Greg Hunt said the best way to deter whalers and minimise the risk of dangerous confrontations would be to have a customs vessel patrolling known or likely trouble spots.

"The sensible action here is to have a cop on the beat," he said.

"The mere fact of an Australian-flagged vessel says to the whalers that we are watching, and says to the protesters: you've got to abide by international maritime law.

"Anything less is just negligent."

But Mr Burke said the opposition's proposal would make the situation even worse.

"Could you imagine what a boost to Japanese whaling it would be if there was an Australian vessel just watching on and nodding," Mr Burke said.

"It's much better that we have taken the legal action that we have taken, that we are in the International Court of Justice, that we are getting closer and closer to decision day there."