Police said the boy, aged eight, was kept locked in a small room in the compound for several weeks and was allowed outside only to do chores.
The compound, located 300km north of Sydney, was hidden beneath an outdoor deck and accessible by trapdoor.
It allegedly contained 225 cannabis plants.
Three other children, aged between one and nine, were also found to be living on the property. All have been placed in care.
It was reported that the three people arrested are the children's mother, her fiance, and the children's uncle.
"The door to the small room in the shed was locked from the outside and police will allege that the boy was mistreated and only allowed out of the shed for chores and sometimes food,'' Detective Inspector Peter McKenna told the Newcastle Herald.
News.com.au quoted police as saying the boy was kept in the room for long periods of time in the past few weeks. The family is understood to have moved into the property earlier this year.
Neighbours interviewed by the Sydney Morning Herald said they rarely saw the boy, though they saw the other children more frequently.
Police from the Manning-Great Lakes command initially struggled to find the bunker when they raided the property on 19 December.
It consisted of three shipping containers buried beneath a hydraulic-powered deck that rolled away at the flick of a switch.
A 28-year-old man and a 26-year-old woman were charged with offences relating to drug cultivation and detaining a person for financial advantage, while a 19-year-old man was charged with drug offences.
The tiny room in which the boy was found contained only a mattress and a bucket for going to the toilet.
Australian police have charged three people after a child was reportedly found locked inside an elaborate underground drugs compound.