Australia's Environment Minister has criticised Japan after pictures emerged showing a dead protected minke whale on a Japanese whaling ship, allegedly in Australian waters.

Photo: AFP

Japanese Prime Minister Shinzo Abe met with Australian Prime Minister Malcolm Turnbull in Sydney over the weekend, when the topic of whaling was mentioned.

The visit coincided with the release of the photos from anti-whaling group Sea Shepherd showing the dead whale on board the Japanese ship.

The group said it happened in Australian waters off the Antarctic coast and urged that country's government to take immediate action.

Josh Frydenberg, who holds the environment portfolio, said the government was "deeply disappointed" Japan had resumed whaling.

In a statement, he said Australia was "opposed to all forms of commercial and so-called 'scientific' whaling".

"It is not necessary to kill whales in order to study them," he said.

"We will continue our efforts in the International Whaling Commission to strongly oppose commercial whaling and so-called 'scientific' whaling, uphold the moratorium on commercial whaling and to promote whale conservation."

Mr Frydenberg's Opposition counterpart, Tony Burke, also issued a statement, criticising the "slaughter under the guise of 'scientific research'".

"Japanese whaling ships have been sighted with their harpoons uncovered in the Southern Ocean, where a moratorium on whaling in currently in effect," he said.

"This is happening in areas Australia recognises as being protected."

Sea Shepherd managing director Jeff Hansen said the government's response was not good enough. "Disappointment isn't going to cut it," he said of Mr Frydenberg's response.

He reiterated figures from a poll in December 2015 that found 80 percent of Australians wanted a customs ship sent to the Southern Ocean to monitor Japan's whaling fleet.

"The Australian people want action, and in the absence of that they're left with Sea Shepherd but it shouldn't be left up to us," he said.

"The Australian government needs to come clean and do the job that they should be doing, defending the whales in the southern ocean whale sanctuary ... Chances are there's been a lot more whales being killed."

Whaling continues despite 2014 ban

Mr Hansen said the fact that this was all happening while Mr Abe and Mr Turnbull had been meeting on Australian soil was particularly disgusting.

"This Japanese whaling fleet is heavily funded and backed by the government of Japan - this is Shinzo Abe's whaling fleet," he said.

"We should be talking tough and saying, 'We're the country with all the resources you guys need, stop sending your whaling fleet into the southern ocean, into the Australian whale sanctuary, turn your boats back home back to Tokyo.'"

In 2014, the International Court of Justice (ICJ) ruled Japan's whaling programme was illegal, prompting a scaled-down version.

But Dr Wally Franklin of Southern Cross University's Marine Ecology Research Centre said Japan continued whaling despite the bans because of concerns about food security.

"Japan is an island - it doesn't have a great deal of land to produce farming commodities," Dr Franklin said.

"They are motivated by the fact that they want to keep the door open to seeking harvest from the ocean as a possible food source.

"But of course that could be solved by the Australian government furthering talks with Japan about providing food security."

New Zealand participated in the ICJ case that ruled Japan's whaling programme illegal, and has continued to state its opposition to it.

- ABC / RNZ