Allegations that Japanese ships have been killing whales within the new Ross Sea Marine Protected Area (MPA) near Antarctica are "frustrating and disappointing", a leading Kiwi scientist says.

At the International Whaling Commission's meeting in Brazil, WWF alleged Japanese whalers had killed more than 50 minke whales inside the MPA over five weeks in January and February this year, just two months after the reserve came into force.

Harvesting krill and fishing is banned in the 1.55 million sq km special protection zone, yet Japan was able to conduct whaling in this unique natural area through a "scientific whaling" loophole.

New Zealand is a member of the IWC and has been a vocal critic of Japan's whaling.

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WWF was on the IWC and the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) to work together with the Japanese government to close the loophole.

"The Ross Sea MPA is supposed to have special protection from human activities to safeguard a wealth of Antarctic wildlife," WWF Antarctic Programme senior manager Chris Johnson said.

"People around the world who celebrated this historic ocean sanctuary will be shocked by the killing of whales within its boundaries.

"Only the IWC can close the loophole that enables whales to be harpooned in a protected area."

Associate Professor Rochelle Constantine, of University of Auckland's School of Biological Sciences, said a recent research trip funded by the Government and The Pew Charitable Trusts provided important new non-lethal data on Antarctica's whale populations.

"One of the most exciting finds from the trip was a mother-calf pair near Scott Island, the same mother with a different calf was tagged in 2012 in New Caledonia," she said.

"Our collaborative research shows how important this region is to whale populations."

Constantine said the Ross Sea region was important for baleen whales feeding on krill.

While scientists knew that krill was an important prey for baleen whales, it was unknown whether humpback whales from the genetically distinct breeding grounds of east Australia and Oceania came together.

The genotype and photo-identification results reveal that there is mixture of whales from New Caledonia, Tonga and east Australia.

These populations are recovering at different rates with some more vulnerable than others, so we needed to consider this when developing protection measures, she said.

"We have been really pleased with the results of this research which shows how important the Antarctic region is to whale species and we need to make sure these fragile populations are free from human threats," Constantine said.

"It is very frustrating and disappointing that the Japanese continue to kill minke whales for research purposes and it is important that countries opposed to Japan's actions, including New Zealand, continue to raise opposition to what is an entirely unnecessary research programme."