"We are working with other like-minded nations to build international consensus against Japanese whaling. We are also exploring options for further legal action," the Australian ministry said.
It added that 32 other nations had lodged protests against Japan's whaling ambitions.
"Australia is committed to the protection of whales. We will continue our efforts in the International Whaling Commission to promote whale conservation and uphold the global moratorium on commercial whaling," the ministry vowed.
The International Whaling Commission banned commercial whaling in 1986. A 1987 agreement, however, allows for whales to be hunted and killed for scientific research purposes – a loophole Japan has been using for decades.