The Australian embassy told the Japanese government Tuesday whaling vessels were not welcome in the country's waters, but the harpoon-equipped whale hunter Yushin Maru No.3 was still there late Wednesday, the Sydney Morning Herald reported.
The Japanese ship was photographed within a few miles of the coast of Macquarie Island, part of the state of Tasmania, officials said.
"I'm aware that there has been one vessel which I'm advised has been in Australian territorial waters and I'll advise that it will leave Australian territorial waters," Prime Minister Julia Gillard said.
The Sea Shepherd anti-whaling group said the whaling ship had trailed its monitoring vessel, the Bob Barker, inside the 12-nautical-mile territorial limit all day.
"It has followed us on circuits of the island, keeping right inside the 12-mile zone," Bob Barker first mate Peter Hammarstedt said.
Don Rothwell, an Australian National University professor of international law, said if Yushin Maru No.3 was remaining close to Macquarie Island it was in violation the U.N. Convention on the Law of the Sea which would normally allow a ship to proceed though those waters.
"The actions of Yushin Maru No.3 are not consistent with the right of innocent passage," Rothwell said.