She was admitted to hospital in a coma 12 days before her death, and it is alleged that brothers Wiremu and Michael Curtis murdered the 3-year-old by kicking her in the head two days earlier.
Dr Stables said Nia's injury was caused by "a substantial degree of force", and possibly a kick to the head.
He said the clot in Nia's head was the result of veins rupturing, leading her brain to swell.
The post-mortem examination had shown a large part of the right side of her brain and some of the left side was dead by the time her life support was turned off.
This cerebral infarction - or brain death - caused Nia's death, Dr Stables said.
He ruled out a brain infection, acute encephalitis, which had been suggested as a possibility when Nia was first taken to hospital.
He said the 3-year-old was 96cm tall and weighed 11.5kg, which was thin for her age and height.
An external examination of her body showed multiple scars, including a 6cm one on her abdomen and healing scabs on her legs, but Dr Stables said there was nothing external that pointed to the cause of death.