Wootton said it is possible it beached itself due to underlying health conditions.
"Even if pygmy sperm whales are refloated, they are more than likely to strand again," he said.
DoC worked with Mana Ahuriri iwi, supported by Trevor Taurima and Chad Tareha, throughout the welfare assessment and euthanasia process.
Wootton said the stranding and death of the whale is a learning curve.
"While this outcome is not ideal, hopefully this will help us learn more about this fairly reclusive marine mammal species," he said.
DoC also works closely with Massey University who are studying pygmy sperm whales.
A DoC spokeswoman said pygmy sperm whales were rarely seen out at sea, but are often found stranded on beaches.
"This is a very common species to strand in New Zealand, but particularly in this area, indicating it likely lived offshore in the Hikurangi trench," she said.
"As they are usually an offshore, deep-water species, it is possible that animals that come close to shore and strand in New Zealand might have underlying health issues."
The spokeswoman said stranded animals of this species often pass away naturally or need to be euthanised.
There have been several sightings of whales around Hawke's bay over the past few months.
Orcas have been spotted swimming around Westshore and Ahuriri on Thursday and throughout November and December.
