Director of Wildbase Hospital Professor Brett Gartrell says they found there was only a thin layer of tissue between the brain and the outside world.
"The CT scan showed that the plates of its skull had not completely fused and the fontanelle was still open.
"The chick was hatched with a hole in its skull that allowed part of the brain and dura (the tough barrier around the brain) to herniate out, the technical term for this condition is a meningoencephalocoele.
"In humans, this spot fuses after birth, but this is highly unusual in birds as the skull has finished fusing prior to hatch.
"The concern was that if this tissue was damaged this would open the brain to trauma and infection.
"With only 144 kākāpō left in the world, this condition could be life-threatening for the critically endangered bird, so action needed to be taken, but nothing like it had been attempted before in avian medicine."
A national group of veterinarians, including veterinarians from Auckland Zoo, Wellington Zoo and Dunedin Wildlife Hospital, conferred to determine that surgery was the best way forward for the chick.
Air New Zealand flew the kākāpō for free to Massey's Wildbase Hospital for the surgery.
Led by Professor Gartrell, a team of veterinarians and veterinary technicians at Massey carried out the pioneering surgery earlier this month.
Professor Gartrell said they based the surgical plan on what is used for this condition in humans and other mammals and then extrapolated these techniques to the peculiarities of avian anatomy.
"This is a risky surgery and the common complications for this surgery in humans include permanent brain damage, continued leakage of cerebrospinal fluid and the possibility of meningitis."
Professor Gartrell described the surgery as intense and said it was only possible because of a national collaboration with vets and conservation workers.
Wildbase Hospital is a dedicated wildlife hospital that runs within Massey University's School of Veterinary Science and provides veterinary services and research to support conservation in New Zealand.
The hospital relies on sponsorship and donations.