Female takahe Paku (13) and male takahe Quammen (15) sat on two fertile eggs taken from Burwood Bush, near Te Anau, in September.
Ecosanctuary conservation manager Elton Smith said staff believed both eggs hatched about five weeks ago, about three days apart.
As the chicks had never been seen together, staff believe the younger chick had died despite its body never being found.
The older chick appeared to be the only one to have been given enough food.
''For all money, it looked like the chick died in the first week,'' Mr Smith said.
Paku had been a mother before, but Quammen had never been a father and it appeared he had not fed the younger chick enough.
Both parents had to constantly fed both chicks to ensure survival, he said.
The parents' sole focus on the older chick for the three days before the second egg hatched would have increased the older chick's chance of survival, he said.
If the chick did not starve, another possible cause of death was by a bird of prey, such as a harrier.
Another possibility was the chick being killed by the stoat living in the ecosanctuary when the egg hatched.
The stoat has since been killed.
But the stoat was ''a fair distance from where the takahe nest is''.
Some chicks died from a ''yolk infection'' but without a body, the cause of death would remain a mystery, he said.
The older chick was healthy and the risk of starvation and infections had passed.
''The biggest risk now is harriers,'' Mr Smith said.
Consequently, the chick spent most of its time hiding in long grass and visitors would be highly unlikely to see it.
The chick had yet to be named and the ecosanctuary would consult relevant groups, such as iwi.
