Australia on Friday branded Japan's killing of 333 whales "abhorrent", saying there was no scientific justification for the Antarctic hunt.

The Japanese fleet set sail for the Southern Ocean in December despite a worldwide moratorium and opposition led by Australia and New Zealand, using a loophole in the ban that allows for lethal research.

On Thursday, Japan's Fisheries Agency announced enough whales had been killed for "scientific research" as the boats returned to port.

"The Australian government opposes so-called 'scientific' whaling clearly, absolutely and categorically," Australian Environment Minister Greg Hunt said in comments emailed to AFP.

"It is in my view abhorrent and a throwback to an earlier age... There is no scientific justification for lethal research."

Japan was forced to abandon its 2014-15 hunt after the International Court of Justice said the expedition was a commercial activity masquerading as research.

Hunt criticised Japan for going ahead with the killings "in spite of a resolution by the (International Whaling) Commission calling on it not to go whaling".

Tokyo claims it is trying to prove the whale population is large enough to sustain a return to commercial hunting, but the meat still ends up on dinner tables and is served up in school lunches.

Environmental activist group Sea Shepherd criticised the Australian and New Zealand governments, saying they had not done enough to stop the whaling.

"The majority of Australians wanted the Australian government to send a vessel to oppose the slaughter. They did not," Sea Shepherd Australia's managing director Jeff Hansen said in a statement late Thursday.

"The governments responsible for protecting these magnificent creatures stood by, in the complete knowledge that both federal and international crimes were taking place.

"This empty response from authorities in the wake of the ICJ ruling is a disgrace."

Some experts say that Japan's refusal to give up the Antarctic mission despite censure by the international court is largely due to a small group of powerful politicians.