He vowed "to bring a permanent end to whaling in the Southern Ocean".
Japan gets around an international ban on commercial whaling by arguing that it harpoons hundreds of whales each year for scientific research.
|Whale meat is sold in Japan, which claims it conducts hunts for research purposes [EPA]
The Australian legal action comes ahead of an annual meeting of the International Whaling Commission in Morocco on June 21, which will discuss a compromise proposal to end years of division among its pro- and anti-whaling members.
The plan would allow Japan - as well as Iceland and Norway, which kill whales in defiance of a 25-year-old moratorium - to hunt the mammals openly if they agree to reduce their catch "significantly" over 10 years.
Australia has criticised the deal, under which Japan's Antarctic catch would go down to 410 whales next season - from about 500 this year - and then 205 in the 2015-2016 season.
Last year, a panel of lawyers and conservationists reported to the Australian and New Zealand governments that Japanese whaling in the Antarctic could be stopped if Japan was held accountable for dumping waste and for undertaking hazardous refuelling at sea.
The panel said the activity violates the 46-member Antarctic Treaty System, to which Japan belongs.
New Zealand has also said it will decide in the coming weeks whether to abandon diplomatic efforts and also file a case in the International Court of Justice against Japan.