The Crown says the boy suffered two head injuries while in their care, and both times was flown to Wellington for craniotomies.
In between these two head injuries, Oranga Tamariki placed the boy in the care of his grandmother in another centre.
By arrangement with Oranga Tamariki, the boy was returned to the couple for Christmas 2019, when he was 4 years old.
He suffered the second, more serious, head injury when he was still with the couple the following month.
The couple have been on bail while their case has been dealt with by the court and will remain so until sentencing, even though the Crown Solicitor, Steve Manning, said he would be seeking prison sentences for both of them.
The neglect charges carry a maximum prison sentence of 10 years; the grievous bodily harm offence is punishable with a maximum of seven years.
Judge Russell Collins told the couple on Friday: "I really need to make it very clear. The Crown position is that a custodial sentence is the appropriate outcome. The fact that I'm giving you bail at this stage is no indication of what the outcome will be."
The abuse and neglect of the child happened between November 2018 and January 2020 and the total of six charges, one of them representative, covered a number of incidents.
The boy suffered the first brain injury in June 2019, from "significant trauma" to his head in the early hours of the morning. It was not possible to establish exactly what caused it and who was responsible.
One of the child neglect charges, against both defendants, was filed because the couple did not seek timely medical treatment for this injury. The boy was taken to Hawke's Bay Hospital at 3.30pm the following afternoon.
He was transferred to Wellington Hospital and underwent a craniotomy to drain blood from between his skull and his brain.
The grievous bodily harm charge against the woman related to the second brain injury, as well as damage to the boy's neck ligaments and retinas, in January 2020.
Around 9.30pm one night, neighbours heard yelling coming from the couple's house.
The man was not at home and a neighbour who ran over found the woman panicking and hysterical, according to the Crown summary.
The neighbour found the boy lying on his back in the hallway, naked and unresponsive and covered in bruises.
An ambulance was called and took the boy to Hawke's Bay Hospital. He was then flown to Wellington Hospital where he underwent another crainiotomy before being flown to Starship children's hospital in Auckland.
The 4-year-old was found to have subdural bleeding on both sides of his brain.
"There was extensive damage to the substance of the brain itself, encompassing the entire right hemisphere as well as some damage to the left hemisphere."
Because of that head injury the boy's life will be "permanently altered in that he will suffer permanent disability", the summary said.
