An initial identification of the creature as a male spade-toothed whale — a species so rare next to nothing is known about it — is subject to confirmation.
Only six specimens had ever been known to science, Doc coastal Otago operations manager Gabe Davies said.
Staff were notified on July 4 a type of beaked whale about 5m long had washed ashore near Taieri Mouth.
It is now in cold storage to preserve the remains until the next steps are decided.
"Spade-toothed whales are one of the most poorly known large mammalian species of modern times," Mr Davies said.
"Since the 1800s, only six samples have ever been documented worldwide, and all but one of these was from New Zealand.
"From a scientific and conservation point of view, this is huge."
Genetic samples had been sent to the University of Auckland and it could take several weeks or months for the DNA to be processed and a final species identification to be confirmed.
The specimen was described as fresh, likely offering the first opportunity for a spade-toothed whale to be dissected.
Te Rūnanga ō Ōtakou chairwoman Nadia Wesley-Smith said the rūnaka would partner with Doc in making decisions about next steps.
"It is important to ensure appropriate respect for this taoka is shown through the shared journey of learning, applying mātauraka Māori [knowledge] as we discover more about this rare species."
The species was first described in 1874 from a lower jaw and two teeth collected from the Chatham Islands.
This sample, along with skeletal remains of two other specimens found at Whakaari White Island and Chile’s Robinson Crusoe Island, enabled scientists to confirm a new species, Te Papa museum has recorded.
Two more recent findings, in Bay of Plenty and north of Gisborne, helped describe the colour pattern of the species for the first time, Doc said.
No live sightings of the whales have ever been recorded.
The species is classified as "data deficient" in the New Zealand threat classification system.
