16/01/2017 8:40 AM AEDT | Updated 16/01/2017 12:33 PM AEDT

Slain Minke Whale Spotted On Japanese Boat In Australian Waters

Australia condemns new Japanese whaling operations.

Sea Shepherd
A dead whale covered in a blue tarp to not be filmed.

CANBERRA – The Australia/Japan relationship is being tested by whaling a day after the Japanese Prime Minister Shinzo Abe finished an official visit to Australia, with the activist environment group Sea Shepherd catching Japanese whalers with the first documented whale kill by Japanese whalers since 2014.

The slaughter of at least one protected minke whale -- shown in Sea Shepherd pictures lying on board the whaling mother ship, Nisshin Maru -- has allegedly taken place in Australian waters in the Southern Ocean.

The killing appears to have taken place over the weekend, coinciding with Abe and Prime Minister Malcolm Turnbull discussing whaling during talks in Sydney.

Environment Minister Josh Frydenberg has condemned the resumption of whaling.

"The Australian Government is deeply disappointed that Japan has decided to return to the Southern Ocean this summer to undertake so-called 'scientific' whaling," the minister said in a statement.

"Australia is opposed to all forms of commercial and so-called 'scientific' whaling."

The Greens have accused the Government of "cowardice" in not pushing Japan harder on whaling while Abe was in Australia.

Labor's Environment spokesman Tony Burke has issued a statement, criticising the "slaughter under the guise of 'scientific research'."

After five weeks of patrolling the southern Ocean, a Sea Shepherd helicopter spotted the factory vessel on Sunday morning with two nearby harpoon ships.

Sea Shepherd
Japanese ship Nisshin Maru found in Australia waters with dead whale on deck.

Upon discovery, Sea Shepherd said the Japanese crew covered their harpoons and the dead minke whale on deck.

It's the first documented whale kill by Japanese whalers since 2014 when the International Court of Justice ruled Japan's whaling operations were illegal. It comes a day after Japan's Prime Minister Shinzo Abe enjoyed an official state visit to Australia.

Brook Mitchell/Pool Photo via AP

Frydenberg has not addressed the alleged location of the whaling action, but Sea Shepherd insists the whalers were operating within the Australian whale sanctuary.

Frydenberg insists Australia will stand firm against any form of 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."

Sea Shepherd
The Japanese harpoon ship, Yushin Maru

"No country has done more to try to end whaling than Australia."

The Sea Shepherd ship MY Steve Irwin is now on an intercept course with the factory ship and the group insists that no further whales will be killed by the whalers.