The intruders used bolt cutters to open a door into the golden lion tamarins' area and then entered the squirrel monkey enclosure.
Some of the small squirrel monkeys were injured, indicating they'd been grabbed and had fought back.
"It's not something I've ever had to come across before, in the 14 years I've been here.
"It took a few seconds for it to sink in, what had happened, and then to think about how to deal with the situation."
The injuries include large bruises and lameness. One monkey had a haematoma on its elbow and others had scratch marks.
Zoo staff decided to let the monkeys recover in their enclosure for as long as possible, in order to calm the sociable critters by keeping them together.
But if they didn't get better soon the injured monkeys would be moved to the Zoo's on-site hospital.
"We've given them some food, as well as some currants for an extra treat for them," Neale said.
"They're starting to settle again, now that things are back to normal, and they're seeing the people they're used to seeing again."
While the monkeys are all disease-free from being in the zoo, a spokesperson said any bites were "highly likely" to lead to infection.
A spokesperson from Wellington Hospital confirmed nobody had been treated for suspicious injuries in the Emergency Department yesterday.
Wellington Zoo Trust chief executive Karen Fifield said staff were concerned by the would-be thieves' sophistication.
"To bring tools like bolt cutters is something that we think is quite pre-meditated," she said.
"They've obviously tried to take a squirrel monkey."
The monkeys would have definitely bitten the intruders, Fifield said.
"The monkeys would have defended themselves. They're quite feisty little animals and they would not have been very happy about a human they did not know in their habitat."
The zoo would not speculate whether the monkeys were being stolen to order. Police and zoo staff were unable to confirm if they had CCTV footage.
Fifield confirmed the zoo had launched an internal investigation and would be increasing security patrols.
Wellington City Council acting chief executive Kane Patena said they'd offered support, particularly any resources the zoo might need for the investigation.
"If there's a will, there's a way. You can put all sorts of security measures in place, but if people are intending on committing crimes they will always try to find a way."
Police completed a scene examination yesterday. Anyone who saw something suspicious should ring Wellington Police on 04 381 2000, or call Crimestoppers anonymously on 0800 555 111.
Although rare in New Zealand, animal thefts from zoo enclosures have happened all over the world.
In 2015 National Geographic reported golden lion tamarins were stolen by professional animal dealers from Zoo Krefeld in Germany.
The magazine reported that in 2011, 400 animals were stolen from European zoos and in 2015, 25 members of the European Association of Zoos and Acquaria reported thefts.
One French zoo had 79 tortoises stolen.
Closer to home, last month Charisma the alpaca was stolen from Dairy Flat, Auckland, leaving his blind mate Bambi adrift.
The alpaca hasn't been found.
In 2008 Hamilton Zoo recovered a stolen pair of Madagascan day geckos and two bearded dragons.
Thieves had cut through chained and padlocked doors to get into the reptile house to steal the lizards.
What is a squirrel monkey?
• According to the Zoological Society of London the primate, also known as Saimiri, is an endangered species that grows to 35m and weigh up to just 1.1kg.
• They have the largest brain of all primates with a brain-to-body mass ratio of 1:17.
• They live together in large troupes of up to 500 and have a polygamous mating system.
• When threatened they make vocal calls, including warning sounds, and have been called "small, nervous primates".
