Sea Shepherd Australia has released confronting footage of a Japanese whaling operation after a five-year legal battle.

Footage shot by Australian Customs personnel in the Southern Ocean in 2008 has only now been made public due to a Freedom of Information fight that began in 2012.

The Australian Government kept the footage secret because of concerns that its release would harm diplomatic relations with Japan.

Sea Shepherd managing director Jeff Hansen says it is a “harrowing” thing to watch.

“You see minke whales swimming at 16, 17 knots to try and outrun these harpoon ships, before being hit with an explosive harpoon that sends shrapnel through their bodies,” he said.

“Hooks come out, and they dive deep, you can see see them diving to try and get away from this cable which they're attached to and they're slowly dragged back to the surface, before they're met with the gunner on the harpoon ship who then shoots them.

“They take a long time to die.”

The footage was taken by officers on the Customs vessel Oceanic Viking when it met with Japan's whaling fleet off the Antarctic coast in 2008.

A legal battle to make it public began in 2012, when the NSW Environmental Defender's Office lodged an urgent Freedom of Information application on behalf of Humane Society International, which was later joined by Sea Shepherd.

Mr Hansen said the footage that Customs handed over initially was of “poor quality” and did not include audio, so further approaches had to be made.

The video evidence was reportedly part of Australia’s case against Japanese whaling ‘research’ in the International Court of Justice (ICJ).

“Initially we were told that we were refused the footage because there was a pending court case,” Mr Hansen said.

“Then once that court case had been settled, and Japan's whaling was found to be illegal, then the reason came out was diplomatic relations.

“In other words, they didn't want to upset Japan. However, the Information Commissioner ruled that the Australian public had every right to see the footage.”

NSW Environmental Defender's Office chief David Morris says it only supports Australia's position on whaling.

“We put forward substantial evidence to the Information Commissioner that the information already in the public domain showed that there wouldn't be the kind of impact on international relations that they were suggesting,” he said.

“For example, Australia had taken the Japanese government to the International Court of Justice on this very issue, and so it was unlikely that this information would cause problems between the two governments of the kind that would justify an exemption.”

Sea Shepherd used to engage in ‘direct action’ against whaling vessels in the Southern Ocean, which included every effort to disrupt and delay the annual slaughter.

Mr Hansen says the recent decision to stop the practice was the right one.

“At the recent International Whaling Commission meeting, Japan stated that they have two enemies in this world — China and Sea Shepherd — and so they devised the program purely aimed at beating us,” Mr Hansen said.

“They've doubled their killing area and lowered their quota down to 333, meaning that even at our best years down there, sending all of our fleet we would struggle to save any whales.

“If we go down there and spend all of our money and resources and don't save any whales, that comes at the expense of so many other vital campaigns that we're doing elsewhere.”

Japan continues to subvert an ICJ ruling that its ‘scientific’ whaling program is illegal, and advocates say they want the latest footage to be used to increase pressure for Japan to be taken to the International Tribunal for the Law of the Sea.

Environment Minister Josh Frydenberg said the Government is pushing Japan to comply with its international obligations.

“At the last International Whaling Commission (IWC) meeting Australia moved two successful motions to increase the international scrutiny of 'scientific' whaling and another to improve the transparency and accountability of the IWC,” he said.

“The Government is considering all avenues to achieve Japan's compliance with the ICJ's judgment and the Whaling Convention.”

An edited clip of the whaling footage can be seen below.