The man, identified in reports as Christophe Champenois, was charged with “murder of a minor” late Sunday in the city of Meaux near Paris, court sources said.
The boy’s mother was charged with failing to prevent a crime and failing to assist a person in danger.
Both were held without bail.
A source connected with the case said the child appeared to have died from “a blow to the head”.
Neighbours said the boy, Bastien, died on Friday after his father put him naked in the washing machine to punish him for getting into trouble at nursery school.
A neighbour who gave her name only as Alice told journalists that she had seen the boy’s body after his mother had come to her apartment for help.
“I took the little boy in my arms, he was frozen, completely naked. He was all white, limp, practically like a toy,” said Alice, who lives in the same apartment building as the couple in Germiny L’Eveque, a town of 1,300 people.
Alice said the boy’s mother had attempted to resuscitate him with heart massage but failed.
A source connected with the inquiry said the man was denying the charges and asserting that the boy had fallen down the stairs.
But witness testimony and tests on the body were “consistent with the fact that the child was put into a washing machine,” the source said.
The source said the father had apparently been punishing the boy for misbehaving at his nursery school and said the child had been repeatedly abused, including by being locked up for hours in a cupboard.