A dramatic high-seas chase has captured the first images of Japan killing whales since Tokyo defied an international 2014 court ruling that declared its Southern Ocean hunt to be illegal.

The photos – taken by anti-whaling activists Sea Shepherd – show a minke whale hauled onto the deck of the giant abattoir ship Nisshin Maru after being speared by a harpoon.

Japan claims its whale hunting is for science, a claim most of the international community dismiss as bogus.

A Sea Shepherd helicopter has tracked Japan's whaling fleet. Photo: Sea Shepherd

A helicopter launched from Sea Shepherd vessel Steve Irwin tracked the Nisshin Maru and two harpoon vessels on Sunday morning after a five-week search for the Japanese fleet.

The whaling crew scrambled to cover the whale carcass with a giant body bag tarpaulin soon after the helicopter buzzed overhead.

Japanese whalers hastily cover the carcass of a whale on the deck of the Nisshin Maru. Photo: Sea Shepherd

"They are definitely hiding what they do," Wyanda Lublink, captain of the Steve Irwin, told Fairfax Media by satellite phone.

"If they weren't doing anything wrong they wouldn't feel the need to hide."

The whale was about to be sliced up on the deck before being stored in freezers below, where it is later sold commercially in Japan.

Crews on board the hunting ships also quickly covered the harpoons as the helicopter flew overhead.

Crew on Japanese hunting ship Yusin Maru cover the harpoon on Sunday after Sea Shepherd activists track the fleet. Photo: Sea Shepherd

Ms Lublink said it was impossible to yet know how many whales had been killed but there had only been a few days of clear weather in recent weeks to carry out the hunt.

Mr Turnbull was accused of turning a blind eye to whaling by conservationists before meeting Mr Abe.

A joint statement by the two leaders made no public mention of Australia's opposition to whaling.

But Mr Turnbull is believed to have raised the issue in private talks with his Japanese counterpart.

The Rudd government challenged Japan's whaling in the International Court of Justice, winning a landmark ruling that found Japan in breach of international law.

A global moratorium on commercial whaling stretches back to the 1980s, but following the 2014 ruling, Japan withdrew from the court's jurisdiction on whaling and declared it would kill 333 minke whales each year.

The Coalition sponsored moves at a global summit on whaling in October to put greater scrutiny on Japanese scientific claims but has also backed away from threats of a further legal challenge.

Sea Shepherd has clashed with Japan's whaling fleet in the past in an attempt to disrupt the hunt, with Tokyo accusing the activist group of sabotage in their controversial high seas protest.

The activists did not sail to the Southern Ocean last year when Japan first resumed whaling after the court ruling. The hunters then killed 333 minke whales, including about 200 pregnant cows.

Ms Lublink said the Steve Irwin is presently about 35 nautical miles behind the Nisshin Maru and has launched its helicopter to track the larger vessel.

The sun shines all hours in Antarctica at this time of year, so Ms Lublink expected the helicopter would keep close watch on the Japanese fleet for at least the coming days.

"If we do lose them, we'll find them again," she said.