Environment Minister Josh Frydenberg has criticised Japan for whaling two days after a meeting between Prime Minister Malcolm Turnbull and his Japanese counterpart.

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

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

Sea Shepherd says crew of the Nisshin Maru scurried to cover the whale with a tarp after being spotted. Photo: Sea Shepherd Global/Glenn Lockitch

The group said it happened in Australian waters and has urged the Government to take immediate action.

Mr Frydenberg said the Australian Government was “deeply disappointed” that Japan had resumed whaling.

In a statement, he said that 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.”

Jeff Hansen from Sea Shepherd said the crew quickly covered the whale with a tarpaulin when their helicopter approached.

“As soon as the whaling fleet saw that Sea Shepherd was on the scene, they were scrambling to cover up their illegal operations, they were covering up their harpoons,” Mr Hansen said.

“This is all happening deep in Australia’s whale sanctuary off the Antarctic coast.

“It shows that even with the Japan Prime Minister on Australian soil, Japan is going about their bloody business ignoring the Australian Federal Court ruling, ignoring the wishes of the International Court of Justice.”

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.”

In 2014, the International Court of Justice ruled that Japan’s whaling program was illegal, prompting a scaled-down version.

-ABC