Jalisco state prosecutors also say the girl was impregnated by her stepfather and not her alleged 17-year-old boyfriend.
Authorities announced last week that a 9-year-old had given birth to a baby girl and that they were looking for her boyfriend.
But prosecutors said Wednesday that DNA tests revealed the baby's father is the girl's 44-year-old stepfather and that he is under arrest.
They said an anthropological study of the girl showed she is between 12 and 13. The girls' parents didn't have a birth certificate for her and initially told authorities she was 9.