Shanahan said that although it was too soon to be certain how the intruder had gained entry, it was likely to be a recent arrival.
A team of staff and volunteers were now laying traps and tracking tunnels across the sanctuary.
The operation will continue until the animal is found and staff are confident that the sanctuary is clear of introduced predators.
Shanahan said the incursion has reinforced the importance of vigilance at the fenced sanctuary.
"A single stoat, weasel, rat or possum could cause significant harm to our birds, lizards and invertebrates. Zealandia is home to many important populations of some of New Zealand's most threatened species, and we must give them the utmost protection."
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.