Only a few Arnoux whales have been discovered washed up around the world, so very little was known about the whale species' anatomy.
Te Papa marine mammal collection manager Anton van Helden said the whale was not a common stranding and not usually seen, although there had been a report of a group of 12 Arnoux whales in Fiordland recently.
"It's mostly been seen around the Antarctic."
It is the largest species of beaked whale in the southern hemisphere.
Having the opportunity to study a whale that had not decomposed meant being able to research such things as diet, he said.
"I would have loved to have been there, but it's a bit difficult getting flights at this time of year."
He hoped to learn about the basic biology of the whale, including the anatomy of its head and how it was different from other Southern Ocean beaked whales.
They also had different stomach structures and ways of making sounds.
"It's a very difficult mammal to study, so every opportunity [is important]."
University of Otago scientists, after consultation with iwi, yesterday took samples from the whale's organs after a digger dragged the whale from the estuary on to the bank.
Department of Conservation biodiversity assets programme manager Dave Agnew said the head and one flipper of the whale had been brought back to be stored in Otago Museum's freezer for dissection in January.
Nothing obvious that could have caused its death showed up, but it was hoped the samples taken might provide an answer, he said.
Doc would return to the site today to bury the whale.
The previous Arnoux whale washed up on New Zealand shores was found at Riverton about six years ago.
Only its front end washed up, but its skeleton was touring the world as part of the Whales Tohora exhibition.
