Australian government counsel Bill Campbell accused Japan of trying to "cloak commercial whaling in the lab coat of science," the Sydney Morning Herald reported.
Campbell said Japan's interpretation of the global whaling treaty allows any nation to decide its own "scientific" kill, with Japan asserting the right to take up to 935 minke whales in the antarctic.
"If each [country] were to act the same way, a total of 83,215 minke whales a year would be killed," Campbell said.
A kill of that magnitude, he said, would be catastrophic for the minke whale population.
Japan will have a chance to respond to Australia's arguments next week.
The country's delegation leader has called Australia's complaint invalid.
"Japan's research whaling has been conducted for scientific research in accordance with international law," said Deputy Foreign Minister Koji Tsuroka.