The Department of Conservation has confirmed the deaths, and operations manager Wayne Costello said it was working with the sanctuary on the matter.
"It’s not presently clear why the tokoeka [kiwi] have died but could be due to environmental conditions or other natural factors which are not yet known.
"We may learn more from further necropsy work.
"The tokoeka were receiving supplementary food and regular check-ups, which is when these issues were discovered.
"Unfortunately, wild animals like tokoeka can be challenging to raise even in managed populations."
Two of the kiwi were found dead in the sanctuary. The other was taken to the Wildlife Hospital Dunedin where it died.
Three other chicks were taken to the Wildlife Hospital Dunedin as a precaution and have since been returned to Orokonui after a check-up found they were healthy, he said.
"We want to acknowledge the efforts of Orokonui staff, who have responded quickly and appropriately, and the support of the Wildlife Hospital Dunedin," Mr Costello said.
"These tokoeka held at Orokonui are part of the Doc-managed Operation Nest Egg programme.
Eggs were lifted from wild areas where they were at risk from introduced predators and hatched in incubators at Willowbank Wildlife Reserve.
The young birds were then looked after at Orokonui to learn the skills needed to be wild kiwi, while receiving supplementary feeding.
Once large enough, they were sent to predator-free islands.
More than 70 kiwi had gone through the Orokonui creche since 2015, including four this season, Mr Costello said.
"Orokonui has contributed significantly to the highly successful out-of-sanctuary management programme and this has helped Haast tokoeka being removed from the list of Nationally Critical birds at the most recent threat-ranking assessment in 2021.
Orokonui is also a kohanga (security) site.
Twenty-four kiwi were released into the wider sanctuary in 2011 and have been breeding successfully.
Orokonui educator Taylor Davies-Colley said it was a "very sad occasion".
"The loss of any taonga species is extremely sad, especially given the work we put into protecting and nurturing them.
"We will continue to work closely with Doc."
