The Australian government said it has lodged a protest with Tokyo after part of the Japanese whaling fleet entered its exclusive economic zone in the Southern Ocean near Macquarie Island.
Canberra is strongly opposed to whaling and launched legal action challenging the basis of Japan's so-called "scientific" hunt in December 2010.
The Japanese fleet left for the Southern Ocean in late December, planning to catch up to 935 Antarctic minke whales and up to 50 fin whales and the Shonan Maru No.2 has strayed into Australian territory.
"The government strongly objects to whaling vessels passing through Australian territorial seas or our exclusive economic zone," Environment Minister Tony Burke said late Thursday.
"Australia has made it clear to Japan on a number of occasions that vessels associated with its whaling programme are not welcome in Australia's exclusive economic zone or territorial sea.
"Our embassy in Tokyo has conveyed these sentiments directly to the Japanese government," he added.
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.
Anti-whaling group Sea Shepherd is again tracking the Japanese fleet, with the militant environmentalist's ships having left from Australia.
On Wednesday, Sea Shepherd said it had located the harpoon ship Yushin Maru No. 3 at a relatively northern latitude and they were now tailing the fleet.
Bob Brown, the founder of Australia's Greens party who assumed leadership of the anti-whaling campaign from fugitive Sea Shepherd founder Paul Watson earlier this month, praised Canberra for raising the incursion with Tokyo.
"This vessel has armed personnel aboard," Brown said in a statement.
"It is an affront to Australia that it is entering our territorial waters surrounding the World Heritage-listed Macquarie Island, which is part of Tasmania."