The boy's suspicious injuries, including widespread bruising and a brain injury, have been previously compared by Detective Inspector Mike Foster to the injuries suffered by murdered 6-year-old James Whakaruru.
Foster had said the boy suffered a sustained beating - possibly over days.
Oranga Tamariki deputy chief executive Children & Families South, Alison McDonald confirmed to Hawke's Bay Today the boy had left rehab.
"The young boy has now been discharged from a rehabilitation centre and we are working with his extended family to determine the best care arrangements for his future," she said.
"Oranga Tamariki has worked with health professionals during his recovery and rehabilitation, and will continue to work alongside his extended family to help keep him safe and well."
The agency could not comment further about who was looking after the 4-year-old boy because of the ongoing police investigation and Family Court matters.
On the day of the family harm incident his stepmother and father, along with some of his extended whānau, were at the property.
No arrests have been made in the case, which has had 10 detectives and significant police resource dedicated to it.
"There have big delays with this due to complexities of the case and seeking medical expert statements," Foster said.
"I cannot make any further comments until we get the medical reports back."
The boy was accompanied by a family member when he was taken by ambulance, initially to Hawke's Bay Hospital, and then to Starship Children's Hospital in Auckland.
He was treated there before regaining consciousness in April and being transferred to a rehab centre.
