A five-metre long spade-toothed whale was found on a beach near the South Island town of Taiari Mouth earlier in July.
A spade-tooth whale has never been seen alive, with only six bodies ever known to science.
"Spade-toothed whales are one of the most poorly known large mammalian species," New Zealand's department of conservation (DOC) spokesman Gabe Davies said.
"From a scientific and conservation point of view, this is huge."
Scientists from DOC and Te Papa, New Zealand's national museum, identified the species as a male spade-toothed whale, and have sent genetic samples to the University of Auckland, responsible for a national archive.
The spade-tooth whale was confirmed as a species based on skeletal remains found in three specimens: on the Chatham Islands and Whakaari offshore volcano of New Zealand, and Robinson Crusoe Island, of Chile.
The recently discovered whale has been taken from the beach and moved to cold storage, awaiting identification and further examination.
In keeping with New Zealand cultural practice, conservationists are working with the local Maori group, Te Runanga o Otakou, to decide on further acts.
"A specimen this fresh offers the first opportunity ever for a spade-toothed whale to be dissected," Mr Davies said.
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