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The call comes as research, which is based on data from a trip to the islands last year by postdoctoral fellow Dr Will Rayment and other Otago University experts, highlights the importance of Port Ross to the New Zealand southern right whale population.
Dr Rayment, who has just returned from another expedition to the islands, said the research published earlier this week showed Port Ross, a sheltered area at the northern end of the islands, was the "primary calving ground for all New Zealand right whales".
This meant the area was important for the overall population of the whale in New Zealand waters and should be protected from "disturbance and development", the research paper said.
Dr Rayment said the area was already well protected as a Unesco World Heritage Site and a marine reserve, but needed further protection in the form of restricted ship speeds in Port Ross.
This came as the latest expedition to the Auckland Islands returned with a photograph of a southern right whale scarred by a ship's propeller.
"We have seen that example of ship strike ... and so if there was some additional regulations about shipping traffic, then that would be beneficial to the whale population."
Dr Rayment said the researchers were surprised to find such a high density in Port Ross despite seemingly ideal areas for southern right whales on the islands.
The research was based on 43 sightings of southern right whale groups made on an expedition to the islands in August last year.
Of the sightings, only eight were made outside Port Ross and all but one of the mother-calf pairs were seen inside the port.