The one-day-old pup was euthanased by Department of Conservation staff yesterday after its mother failed to bond with it and left it in the shallows of St Kilda, after giving birth on Tuesday.
The pup would have drowned had it not been for the quick actions of Dalton Williams, of Dunedin, who saved it from the water after becoming possibly the first person in the world to witness the birth of a leopard seal.
Niwa researcher and leopard seal specialist Krista Hupman said she ''jumped on the first plane possible'' after hearing about the occurrence.
''We arrived at first light and saw it with its mother so we thought there was still hope.''
The mother left soon after.
When the eyes of the ''very small'' seal, which she believed could have been premature, closed, it became obvious even if its mother returned it would be unable to suckle.
Little was known about leopard seal pups because ''only a handful'' had been studied since the 1900s, Dr Hupman said.
''We don't know if the behaviour of the mother was unusual or not, or if the pup was premature but it certainly appeared to be small in size and underweight.''
Scientists had been unable to tell the gender of the pup yet.
The seal would not have experienced any pain when it was euthanased and the case would provide valuable information on the species, she said.
''We are trying to raise the profile of leopard seals in New Zealand.
Nearly all leopard seal pups are born in the Antarctic.
A spokeswoman for Leopard Seal Sightings New Zealand said in a statement it was a ''terribly emotional time'' for everyone involved.
Department of Conservation ranger Jim Fyfe said while it was ''a sad end for the pup'' it was a good example of the community doing all it could to save a rare animal.
''The Dunedin City Council and its contractors limited vehicle and public access to the mother and pup, while members of the public and New Zealand Sea Lion Trust volunteers kept a watchful eye over it and alerted dog-walkers and passers-by to its presence.''
The Department of Conservation would work with local iwi and Dr Hupman to decide the next step.
The pup's body was being stored at Otago Museum.
The last leopard seal pup to be seen in New Zealand was on the Coromandel Peninsula in 1977.