Japan's latest whaling expedition into the Southern Ocean has again drawn heavy criticism from the Government, which has called for Antarctica's marine ecosystems to be better protected.

A fleet left Japan this week for the polar region, where it planned to kill 333 minke whales.

It was Japan's fourth expedition since the country temporarily ceased whaling when the International Court of Justice ruled, on the back of a case brought by Australia and New Zealand, that its programme was "not for purposes of scientific research".

Yet that hadn't stopped Japan continuing to kill whales under what's been widely criticised as a guise for commercial whaling.

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Japan had attempted to resume commercial whaling of some species including minke whales, but its bid was voted down by the International Whaling Commission (IWC) in September.

In a statement today, Foreign Affairs Minister Winston Peters said the programme rather went against scientific advice, along with growing support for greater protection of the ocean's ecosystems.

"New Zealand is deeply disappointed that whaling continues in the Southern Ocean despite the significant scientific advice against this outdated and unnecessary practice," Peters said.

"It's difficult to understand when Japan has so much to offer the world it would compromise its potential for goodwill with such an outdated practice."

Otago University marine scientist Professor Liz Slooten, who has been a member of the IWC's scientific committee since 1992, also condemned the programme.

Slooten was heavily critical of Japan's position that its whaling was scientific, citing dozens of journal articles rejecting the stance, and said the committee was growing increasingly impatient.

But due to the IWC loophole, Japan could continue whaling freely, with no opportunity for the IWC to even modify its catch target.

Slooten argued whaling was neither sustainable nor humane, and also questioned why Japan continued to damage its reputation over the practice.

"These are slow-breeding, long-lived, highly intelligent social mammals – short of a chimpanzee, they're the worst thing you could think of eating," she said.

"This practice should have gone out decades ago, if not 100 years ago."

Peters said now was the time to increase protection of pristine Antarctic ecosystems – a goal this month dashed when Russia, China and Norway failed to support proposals to establish three major new sanctuaries around the continent.

"We must stop the killing of whales in the name of science."