Head ranger Kelly Gough said the ecosanctuary sustained "significant damage" from the storm on Friday, including slips blocking culverts and diverting water through the predator fence surrounding the ecosanctuary in Waitati.
The water lifted the fence mesh, causing at least three "small breaches" to form.
Any predator would have struggled to enter the ecosanctuary through the breaches because of the force of the stormwater running them, Ms Gough said.
But wildlife in the ecosanctuary might have got "caught out and drowned" by the storm, especially those living in burrows.
Kiwis lived in burrows but they should have been able to get out in time, she said.
"But animals like tuatara might be more vulnerable."
Ecosanctuary staff would be checking on the wildlife this week.
Volunteers started temporary repair work on the damaged fence about 8am on Saturday.
The ground needed to dry and a digger was required for the "long-term fix".
"A big digger will have to lift a little digger over the fence to get to a section where it has slipped," Ms Gough said.
Storms had damaged the fence three times before but this weather event was the "worst for Orokonui" since the fence was built in 2007.
"We’ve seen it before but not on this scale."
