Facing Melbourne Magistrates Court, Gursewak Dhillon, 23, was remanded in custody to appear for a committal hearing on June 29.

Clean-shaven and dressed in a white polo shirt, Dhillon did not apply for bail and nodded politely when Deputy Chief Magistrate Jelena Popovic explained he could still do so through his lawyers.

Dhillon's wife, Sim Kaur, sat in court with a black shawl draped around her shoulders during the brief hearing.

An obviously tired Ms Kaur watched intently as her husband surveyed proceedings from the dock.

Speaking to The Age before the hearing, Ms Kaur said: "Everything has gone wrong."

However, she said due to police advice she could not elaborate.

Gurshan Singh's body was found dumped in grass at Oaklands Junction, near Melbourne Airport last Thursday.

The toddler had vanished from his Lalor home, about 20 kilometres away, about six hours earlier.

Police allege that Dhillon, who shared the home with Gurshan’s parents and others, placed the boy unconscious but alive in the boot of his car, drove him in the boot for at least three hours and dumped him at Oaklands Junction without checking to see if he was alive or dead.

An autopsy has not revealed the cause of death.