The intruders used bolt cutters to open a door into the Golden Lion Tamarins area and then entered the squirrel monkey enclosure.
"They've obviously tried to take a squirrel monkey," said Fifield.
Staff checked the habitat several times before contacting police and issuing a media statement saying the monkey was missing and staff were concerned for her welfare.
However, about 12.20pm a zoo spokesman confirmed the animal had been found, hiding in her enclosure.
"We had one that we thought was missing but she was hiding, obviously very scared," said Fifield, during a media conference this afternoon.
Although all of the squirrel monkeys were now accounted for, some had been hurt during the break in. The animals are being checked by a vet tomorrow.
The monkeys' injuries indicated they had been grabbed, 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 that they did not know in their habitat."
One monkey had a haemotoma on its elbow and others had scratch marks.
The monkeys would have definitely bitten the alleged offenders, Fifield said.
The zoo would not speculate whether the monkeys were being stolen to order and said they did not have CCTV footage of the incident.
The outside security fence was not breached, but a contractor left a service gate unlocked.
"However, because [the intruders] had bolt cutters they would have got through that bolted gate anyway."
When asked what prices squirrel monkeys could fetch, Fifield said the zoo did not put monetary values on its animals.
"To us they're priceless."
The incident had distressed staff.
Squirrel monkeys were social animals and would be terrified if they were stolen and were separated from their mates.
"We want to say to whoever tried to do this, this is really just not acceptable and it's not appropriate to try to take one of these animals," said Fifield.
The zoo said in a statement earlier this morning when one of the monkeys was still believed to be missing that it wouldn't have pressed charges or asked questions if the alleged offenders had returned the animal.
Fifield confirmed zoo has launched an internal investigation and would be increasing security patrols.
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.
At the time the director of the Association of Zoological Gardens in Germany, Volker Homes, said zoo thefts were "a really severe problem".
Closer to home, last month Charisma the alpaca was stolen from a Dairy Flat, Auckland, property, leaving his blind mate Bambi adrift.
The alpaca hasn't been found.
In December 2016, The Sun reported a group of teenagers broke into London Zoo at night and filmed themselves exploring the enclosures.
One teenager was bitten by a llama during the escapade, while another leapt into a penguin enclosure.
The escapade was later posted on YouTube.
In 2008 Hamilton Zoo recovered a pair of Madagascan day geckos and two bearded dragons which were stolen.
Thieves 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 1100g.
• They have the largest brain of all primates with a bran to body mass ratio of 1:17.
• They live together in large troops 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".
