For the first time more habitat for the critically endangered birds is needed.
Heritage and museum manager Tony Roxburgh said the study could have a significant impact on the Maungatautari project and the biodiversity of Waipā.
"Kākāpō have the ability to climb the traditional pest proof fencing which would leave them exposed to predators should they decide to climb out," he said.
"This project will look at using an alternative fencing system to prevent that from happening.
"Sanctuary Mountain and their partners will test things like how the kākāpō react to the fencing and whether the birds would need extra technical aid that would prevent them from getting too close to the fence."
The project is being jointly funded by Gallagher Group Limited, Land Care Research, MEIT and Waipā District Council.
Tony said Maungatautari was the ideal spot for kākāpō as there was "a large enough area of land and ample vegetation to support a thriving population".
The space was also largely free of mammalian pests.