"The fact that the Japanese crew went to cover up their harpoons and the dead minke whale on deck just shows that they know what they're doing is wrong", Wyanda Lublink, the captain of the group's 59-meter flagship Steve Irwin, said in a Sea Shepherd statement.
The marine conservation group Sea Shepherd has released footage of Japanese factory whaling ship Nisshin Maru with a dead minke whale on its deck.
"It is not necessary to kill whales in order to study them", he said.
But Sea Shepherd managing director Jeff Hansen said the government's response was inadequate.
"No country has done more to try to end whaling than Australia".
Environmental activist group Sea Shepherd has tracked down the Japanese whaling fleet in the Antarctic, taking the first photographs of dead whales since an worldwide court decided Japan was breaking the rules.
"When they were in opposition, the government said there was blood in the water and a blind eye in Canberra".
It comes two days after Japanese Prime Minister Shinzo Abe arrived in Sydney to bolster defence ties with Australia.
Sea Shepherd has tweeted a picture of a slaughtered whale lying on board Nisshin Maru.
Frydenberg has clarified that Australia is against scientific whaling.
Australian Greens Senator for Tasmania Nick McKim said that "Japan should not be let off the hook" and the global community need to enforce the jurisdiction of the worldwide Court of Justice.
Until officials in Australia, the International Whaling Commission, or the International Court of Justice figure out what they want to do about illegal whaling, it's a good thing we've got conservationists on the case, so at least this one death hasn't gone unnoticed.
"I think our view is pretty well known and we would take the same sort of view as Australia on this", said English, who is on his way home from his first trip to Europe as Prime Minister. Japan does not recognize Australia's territorial claim on the waters off Antarctica and has continued hunting whales despite worldwide efforts to stop the hunt.
Labor spokesman Tony Burke said the government had been "absent on this issue for too long".
Because of scientific whaling research, Japanese whalers still kill hundreds of whales every year - many of them in the waters of the Southern Ocean.
Sea Shepherd has clashed with Japan's whaling fleet in the past in an attempt to disrupt the hunt, with Tokyo accusing the activist group of sabotage in their controversial high seas protest.