SA police to speak with missing Perth toddler's father

South Australian police will speak to the father of a missing Perth toddler, once he has recovered from heavy sedation at a hospital in Perth.

Three-year-old Imran Zilic was reported missing by his mother after he failed to return home in Perth following a two-day custody visit with his father, Aalia Zilic

The boy's father was taken to Perth heavily sedated and under police guard after being arrested in Kununurra in Western Australia's north on Saturday.

Mr Zilic is being detained by West Australian police under a mental health order and will be questioned, although so far he has refused to divulge the boy's location.

SA police are still searching for the boy among thousands of mine shafts in Coober Pedy in that state's north, but have not ruled out foul play.

A t-shirt the boy was wearing before his disappearance has been found, but forensic testing has provided no further evidence.

The toddler's disappearance has been declared a major crime in South Australia, although police have not yet laid charges.

Detective Inspector Doug Barr says the boy's father has not cooperated with police so far.

"We have not charged any person in relation to the disappearance of Imran Zilic," he said.

"We would encourage members of the community that we're still looking for Imran Zilic, he may well be somewhere in Coober Pedy."