Government MP Warren Entsch said it was inconsistent to allow Aborigines to kill sea mammals such as turtles on cultural grounds but to oppose any form of whaling.
Entsch is parliamentary secretary for tourism, representing an industry which opposes whaling on the grounds that it could damage a whale-watching industry worth hundreds of millions of dollars a year in Australia.
"I'm not totally against allowing indigenous hunting of our sea mammals but, if the government wants to be consistent about the need to impose total prohibition on whalemeat, then they need to do exactly the same with dugong and turtle in our own country," Entsch told the Australian Associated Press.
"Humpback and fin whales shouldn't be touched because they are clearly endangered and they do not have the capacity to cope with any form of harvesting.
"But there could be an argument for sustainable, managed take of some of the more prolific species such as minke."
His comments came as Australian officials played a key role in rejecting Japan's push for a resumption of commercial whaling at an International Whaling Commission (IWC) meeting in Ulsan, South Korea.
Opposition enviroment spokesman Anthony Albanese said Entsch was undermining Australia's position.
"At a time when the Australian government, at great expense, is lobbying countries in the IWC, it is an absolute outrage that the parliamentary secretary for tourism is undermining Australia's position at that meeting," he told reporters.