This is the shocking evidence of a Japanese whaling hunt in an Australian whale sanctuary that the federal government did not want you to see.

After a five-year freedom-of-information battle, marine conservation group Sea Shepherd has obtained unreleased footage, shot by Australian customs officials, which reveals in distressing detail the killing of a minke whale by a so-called Japanese "research" ship.

The federal government fought to have the footage kept secret, arguing that it would harm relations with Japan - prompting accusations it prioritised diplomatic interests over protecting the whales and representing the views of Australians who want the annual killing spree stopped.

Japanese whaling vessels earlier this month departed for the Southern Ocean.

Sea Shepherd Australia managing director Jeff Hansen has demanded the government honour a pre-election pledge to send a customs ship to Antarctica to police the hunt, which takes place in Australian waters in contravention of international laws.

"This footage shows the bloody brutality, cruelty and senseless killing of such beautiful, intelligent and majestic animals," Mr Hansen said.

"These whales are hunted down, before being hit with an explosive harpoon that sends shrapnel through their bodies, while prongs come out so that the whale cannot escape."

The footage was shot by officials on board the customs ship Oceanic Viking in January 2008 to support possible future legal action.

Environment Defenders Office NSW in 2012 sought access to it on behalf of Sea Shepherd. Officials refused several times to hand it over, citing the potential harm to relations between Australia and Japan. Earlier this year the Australian Information Commissioner ordered the immigration department to release the footage.

Mr Hansen said by seeking to keep the footage secret, the government "has chosen to side with the poachers instead of defending the whales of the Southern Ocean".

Sea Shepherd is also calling on the government to take Japan to the International Tribunal For the Law of the Sea.

In February 2013, then opposition environment spokesman Greg Hunt accused the Labor government of "turning a blind eye to whaling in our waters ... [we] should have a Customs vessel in the Southern Ocean."

Since coming to power the Coalition has not dispatched any such vessels, but has sent a plane to conduct aerial surveys.

In January this year, Japan was caught killing a whale deep inside Antarctic waters declared by Australia to be a protected whale sanctuary.

Sea Shepherd announced in August it no longer had the resources to send its boats to prevent the hunt.

A spokesman from the Japanese embassy said its whale "research" program was carried out "in accordance with the International Convention for Regulation of Whaling".

Japan reportedly intends to take about 4000 whales over the next 12 years and ultimately plans to resume commercial whaling. It claims the whaling is for scientific research - yet also allows the sale of the whale flesh in markets and restaurants.

EDO NSW chief executive David Morris said Australians had a right to see the footage and transparency about what the government knows about unlawful whaling in Australian waters was "a matter of clear public interest".

Environment Minister Josh Frydenberg said the government was "deeply disappointed that Japan has decided to return to the Southern Ocean this summer to undertake so-called 'scientific' whaling as it is not necessary to kill whales in order to study them".

"The government will continue to advocate for Japan to comply with its international obligations and the principles set out in the International Court of Justice's judgment," he said.

Mr Frydenberg said Australia moved two successful motions at the last meeting of the International Whaling Commission to increase the international scrutiny of "scientific" whaling.