Police say that after arguing with the girl's mother, Noel Morales waited until the woman left to go to work before attacking their daughter while she was playing in her bedroom.
He left the child with bruises on her stomach, liver and arm, police say.
According to court documents, Morales told police he "didn't know what happened" but also that he "punished" the child.
The judge also asked prosecutors to turn over video of a confession Morales made while in police custody.
Morales is due back in court on June 26.