Police have removed from a South Australian mine shaft a body believed to be that of missing Perth toddler Imran Zilic.

Police spokesman Senior Constable Mick Turnbull said the body would be brought to Adelaide later on Saturday for formal identification.

"They removed him from the mine last night and did some forensic investigations," Sen Const Turnbull told AAP.

"It's anticipated that they'll bring him, the boy, back to Adelaide some time today."

The toddler's body was on Friday discovered inside a seven metre deep mineshaft about 47km south of Coober Pedy, near the Stuart Highway in northern SA.

It is unknown how long the child had been in the mineshaft before his body was found or if he was dumped there alive.

While the body has still to be formally identified, Detective Inspector Doug Barr has said it was thought to be that of the three-year-old, taken from his Perth home on April 20 by his father Aliya Zilic.

It was believed Mr Zilic had left his son in Coober Pedy, sparking fears for the child's safety and prompting pleas from the boy's mother for his return.

Police on Friday refused to comment on precisely what information led them to the mine shaft, or whether Mr Zilic had co-operated in the discovery.

The boy's father has been held under the mental health act in Perth since being arrested in Kununurra, in far north Western Australia, last week.

Detective Inspector Barr said forensic officers and a pathologist spent the night in the Coober Pedy area and that officers soon planned to arrest a suspect interstate.