Environment Minister Melissa Price says Australia would "strongly prefer" Japan remains in the International Whaling Commission amid reports the country will withdraw.
Japanese news agency Kyodo has reported, citing unnamed sources, that the country could leave the commission as early as next year.
The government in Tokyo is understood to have been mulling leaving the whaling commission for some time.
Ms Price says she is aware of reports surrounding Japan's imminent departure.
"While we would strongly prefer Japan to remain a party to the convention and a member of the commission, the decision to withdraw is a matter for Japan," she said.
"Australia remains committed to the commission and acknowledges its crucial role as the pre-eminent international body responsible for the conservation of whales and the management of whaling.
"We will continue to work through the commission to conserve whales, and remain opposed to all forms of commercial and so-called 'scientific' whaling."
A spokesman for Japan's Fisheries Ministry told the DPA news wire that nothing has been decided yet.
At its annual meeting in Brazil in September, the International Whaling Commission rejected a Japanese proposal to lift a 32-year-old whaling ban.
At the time, Japanese Fisheries Vice Minister Masaaki Taniai said Tokyo had no choice but to examine all possible options.
Greenpeace Australia Pacific condemned the news and urged Australian Prime Minister Scott Morrison to step in.
"This snub to multilateralism is unacceptable and deeply concerning, but let us not forget that the Japanese fleet has been conducting commercial whaling under the guise of scientific research for many years," Greenpeace senior campaigner Nathaniel Pelle said.
Japan is under pressure from local fishermen to restart commercial whaling.
The IWC agreed to a moratorium on commercial whaling in 1986 to protect whale populations on the brink of extinction.
Japan nevertheless kills an estimated 450 whales annually.
Labor environment spokesman Tony Burke said the Australian government should seek legal advice on what Japan's decision means for the moratorium.
"The Japanese whaling fleet left for the Southern Ocean in November and may already be slaughtering whales," he said.
"This needs to end."
