Grenoble prosecutor Jean-Yves Coquillat said investigators found some of Maelys De Araujo's remains on Wednesday in a snow-covered ravine.
She went missing in August when she was a guest at the wedding in Pont-de-Beauvoisin, near the mountain city of Chambery.
The prosecutor said chief suspect Nordahl Lelandais told investigators on Wednesday that he killed her accidentally, hid the body and then returned to the wedding party before eventually dumping the body in the ravine.
The prosecutor said Lelandais did not explain the circumstances of the girl's death.
A former army dog handler, Lelandais had already been charged in her disappearance.
One guest at the wedding, called Gregory, spoke to Le Parisien at the time of the disappearance.
He said: "The DJ for the evening announced on the microphone that a child had disappeared. Suddenly, everyone started searching, in the main hall and outside.
"It was anguish. To see the disappearance of a nine-year-old, that's not nothing. We initially thought she must be asleep in a corner after a game of hide-and-seek. After an hour, as we'd found nothing, the police were alerted."
Police reportedly scoured the area using a helicopter and dogs, as well as interviewing all 180 wedding guests.
Additional reporting by the Press Association
