The Australian government Friday lodged a protest with Tokyo after a ship from 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, a support vessel, strayed into Australia's economic zone Thursday.
"The government strongly objects to whaling vessels passing through Australian territorial seas or our exclusive economic zone," Environment Minister Tony Burke said.
"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.
Japan's Fisheries Agency said it was aware of the Australian statement but when asked to confirm if a ship had entered the Australian zone, an official only said: "We are carrying out the mission under international law."
He declined to comment further in consideration of "the safety" of the Japanese fleet.
Anti-whaling group Sea Shepherd is again tracking the 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.
Its sister ship Bob Barker was pursuing the Nisshin Maru factory vessel, but officials said it had lost it and the Shonan Maru No.2 was shadowing the Bob Barker when it sailed into the economic zone.
"When the Sea Shepherd ship Bob Barker made contact with the factory ship, this ship (Shonan Maru) tailed Bob Barker and has been doing so for a couple of days," said Bob Brown, who assumed leadership of the anti-whaling campaign from fugitive Sea Shepherd founder Paul Watson earlier this month.
Brown, the founder of Australia's Greens party, praised Canberra for raising the incursion with Tokyo.
"This vessel has armed personnel aboard," he said.
"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."
The Australian government revealed in December its legal challenge to Japanese whaling through the International Court of Justice should be heard this year.
It said both Canberra and Tokyo had filed their detailed written arguments with a hearing in The Hague anticipated in the latter half of 2013.