Emile Soleil, aged two-and-a-half, was at the summer home of his grandparents in the tiny hamlet of Le Haut-Vernet when he vanished in July.
Dozens of gendarmes and investigators, aided by dogs specialised in detecting human remains, were involved in the search which will also seek to find new evidence about what happened to Emile, the local gendarmerie told AFP.
It remains unclear what happened to Emile, with possibilities ranging from an accidental fall to manslaughter to murder not ruled out.
Searches will continue for as long as necessary, the gendarmerie has said, with no outside person allowed to access Haut-Vernet, home to just 25 people, until the end of this week at least.
Investigators on the ground are being helped by forensic colleagues in Paris who are examining the remains that were found.
The remains - the skull and teeth - were found on Saturday by a hiker along a track some way from the hamlet of Le Haut-Vernet, with the key question whether that was the place Emile died or if they were moved there later.
That area had already been thoroughly inspected shortly after Emile went missing in July.
Investigators will try to find out whether "these bones could have been moved by a human, an animal, or the weather conditions," gendarmerie spokeswoman Marie-Laure Pezant said on Monday.
Two neighbours last saw Emile walking alone on a street in Le Haut Vernet, 1,200 metres up in the French Alps on July 8th. The little boy was wearing a yellow T-shirt, white shorts and hiking shoes.
A massive search involving police, soldiers, sniffer dogs, a helicopter and drones failed to find any sign.
Police last week returned to the village, cordoning off the area and summoning 17 people including family members, neighbours and witnesses to re-enact the last moments before he went missing.
There is no suggestion of any link between the timing of the re-enactment and discovery of the remains.
Emile's mother and father were absent on the day of his disappearance. "This heartbreaking news was feared," the child's parents said in a statement released by their lawyer after the remains were found.
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