Canberra is strongly opposed to whaling and launched legal action challenging the basis of the so-called "scientific" hunt in December 2010 after failing to persuade Tokyo to halt the cull of almost 1,000 animals through diplomatic channels.
Japan claims it conducts vital scientific research using a loophole in an international ban on whaling, but makes no secret of the fact that the animals ultimately end up on dinner plates.
New Zealand formally applied to join Australia last month, with the two countries arguing that the slaughter is needless and has no scientific merit.
"The Australian government condemns all commercial whaling, including Japan's so-called 'scientific' whaling," Environment Minister Tony Burke said Saturday.
"It is particularly offensive that Japan's whaling will take place in the Southern Ocean Whale Sanctuary established by the International Whaling Commission.
"We will keep working to achieve a permanent end to all commercial whaling."
His comments came as Japanese whaling vessels left port Friday on a collision course with militant environmentalist group Sea Shepherd, which has vowed to stop the hunt and has four ships bound for the Southern Ocean.
The fleet's departure comes weeks later than expected and days after a US court ordered Sea Shepherd to stay at least 500 yards (metres) from whaling vessels.
Citing the Fisheries Agency, Kyodo News reported three vessels left from the far-western port of Shimonoseki, while environmental group Greenpeace said the whaling fleet's main ship departed from another port.
Japan is aiming to catch 935 Antarctic minke whales and up to 50 fin whales, the fisheries agency said earlier.
Australian Foreign Minister Bob Carr said the stand against commercial whaling was shared by the international community.
"The International Court of Justice is an appropriate forum for a resolution for this issue," he said.
"We're matching words with action in pursuing this matter before the court. And we do so with the support of the majority of nations in our region and around the world."
Both Canberra and Tokyo have filed their detailed written arguments in the International Court of Justice, he added.
The court will now set the case down for a hearing in The Hague with Australia anticipating it will be listed for the latter half of 2013.