The child was malnourished and could no longer walk because he had been in a seated position for so long.
The boy was taken to the hospital, and his father was detained.
Police were alerted by a neighbour to "sounds of a child" coming from a van on Monday in the village of Hagenbach near the borders of Switzerland and Germany, according to a statement from Prosecutor Nicolas Heitz.
After forcing the van open, they found a child "lying in a fetal position, naked, covered by a blanket on top of a mound of rubbish and near excrement," the statement said.
The boy's father told investigators that he put the child in the truck in November 2024 "to protect him," because his partner wanted to send the boy to a psychiatric hospital, the prosecutor said.
The boy was seven at the time.
The prosecutor said there was no medical record that the boy had any psychiatric problems before he disappeared, and that the boy had had good grades in school.
The boy told investigators that he had "big difficulties" with his father's partner, and thought his father "'had no choice" but to lock him up, according to the prosecutor.
He said he hadn't showered since 2024.
The father was handed preliminary kidnapping and other charges and kept in custody.
His partner denied knowledge that the boy was in the van, according to the prosecutor.
She was handed preliminary charges, including failure to help a minor in danger, and released under judicial supervision.
The boy's 12-year-old sister and the 10-year-old daughter of his father's partner were put in the care of social services.
The prosecutor's office is investigating whether others were aware of the locked-up boy.
Friends and family told investigators they thought the boy was in a psychiatric institution.
His teachers were told he had transferred to a different school, according to the prosecutor's office.
Authorities did not release the names of the victim or family members.
Residents of the village reached by The Associated Press expressed shock on Saturday at what happened and said they were unaware of the boy's whereabouts.
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