SA police end probe at toddler's grave

Police have wound up a forensic probe at three-year-old Imran Zilic's mine-shaft grave near the opal town of Coober Pedy in outback South Australia.

They will now formally charge the boy's father with murder, having been granted an application for the arrest of Aliya Zilic in an SA court late on Friday.

Mr Zilic has been held under a mental health provision in a Perth hospital since shortly after being questioned over Imran's disappearance by police last week in Kununurra, in the far north of Western Australia.

SA police on Sunday could not say when they would formally charge Mr Zilic in a Perth court and escort him back to Adelaide.

"But once they have executed the warrant then we can move to extradition," an SA police spokesman said on Sunday.

Imran, who did not speak English, was taken by his father on a two-day custody visit from his mother Mirsada Halilovic's Perth home on April 20.

He was later reported missing. Police said he was last seen on April 21, when he and his father checked into Poochera Hotel on the Eyre Peninsula in SA.

Mr Zilic was detained by police in Kununurra, 3,200km north of Perth, on May 1.

Police feared Mr Zilic had left his son in Coober Pedy, sparking a search for Imran and pleas from Ms Halilovic for her son's return.

Last weekend, SA police discovered a T-shirt belonging to Imran in a dugout-style house in Coober Pedy.

The toddler's body was found on Friday inside a seven-metre-deep mine shaft about 47km south of the town.

Imran's remains have been retrieved and flown to Adelaide for autopsy and formal identification.

Officers have completed a forensic examination at the mine shaft, after scouring the surrounding area for evidence.

SA police would not comment on reports the forensic investigation showed Imran was already dead when he was left in the shaft.

Imran's mother in Perth is understood to be distraught.

But an unnamed family spokesman said the family was thanking everyone who had helped them, in a statement to the Seven Network.

"The little boy is dead," the statement said.

"Nothing will bring him back.

"We've thanked everyone who helped us."