"It is extremely upsetting and disappointing to see someone target the fence in this way. It protects countless rare and threatened species, including kiwi pukupuku, hihi/stitchbird, tīeke/saddleback, titipounamu/rifleman, tuatara and more." said Zealandia chief executive Paul Atkins.
"The sanctuary has played a huge role in improving birdlife across the city, and the specially designed fence is critical for giving these species a safe space to establish."
The hole, measuring about 15 cm high by 10 cm wide, is of a sufficient size to allow access for rats, mustelids or other predators of native New Zealand species, many of which are just starting their breeding season.
"At this point we are unable to pinpoint exactly when the damage was done. We do very frequent fence checks, so it was most likely over the weekend," said Dr Danielle Shanahan, the director of Zealandia's centre for people and nature.
Zealandia is now mounting a precautionary incursion response in case any predatory mammals did enter following the damage. This includes setting trapping lines and cameras to identify intruders.
"The Zealandia fence line is a popular walking track, and we are appealing to the Wellington public to report any vandalism they witness to the police. There is also a phone number to report damage at many locations along the fence line."
Zealandia is now looking at additional security measures that can be installed, such as CCTV to prevent future damage.
Shanahan said she was "really nervous" at the possibility a predator had managed to get into the sanctuary.
"Even one stoat, for example, could decimate an entire population of a threatened species.
National's candidate for Wellington central Nicola Willis said she was "outraged", and that Zealandia was a "jewel in Wellington's crown".
"So many in our community have helped contribute to this local conservation effort ... to see some lowlife put all that at risk is just hugely disappointing.
"Mess with our fence and you're messing with everyone in Wellington."
One in five Wellingtonians trap pests in their own backyards, she said.
"[This is] a kick in the guts to all the Wellingtonians who are doing their best to conserve our native birds and I join them in condemning this behaviour.
"It's absolutely unacceptable and despicable behaviour."
Zealandia was last year named one of Time magazine's World's 100 Greatest Places of 2019.
For 24 years, Zealandia has been working to restore a valley located just 2km from downtown Wellington, with the vision to restore its forest and freshwater ecosystems as closely as possible to their pre-human state.
Zealandia is a 225ha ecosanctuary that was fenced in 1999.
Since predators were eradicated, it has reintroduced 20 species of native wildlife back into the area, including six extinct on mainland New Zealand for over a century.