Chief executive of Wellington Zoo Trust Karen Fifield told media yesterday that the break-in looked premeditated because bolt cutters had been used to access the enclosure.
She said the monkeys would have bitten the alleged offenders.
"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."
At first the zoo feared the intruders had stolen a female squirrel monkey but they were later able to confirm she had been hiding all along.
"We had one that we thought was missing but she was hiding, obviously very scared," said Fifield.
Anyone who had seen something suspicious was asked to ring Wellington Police on (04) 381 2000, or to call Crimestoppers anonymously on 0800 555 111.