The crime took place yesterday when the victim had gone to the church for taking Bible lessons, they said.
The accused, Fr Devaraj (65), of Kandanthitta CSI church will be produced before a magistrate later in the evening.
A case under POCSO (Prevention of Children from Sexual Offences) Act and section 376 of IPC (rape) has been registered against the priest, police said.
The girl's father alleged that he saw his daughter being abused by the accused when he came to pick her up, and immediately informed the police.