Fr Robin Mathew of St Sebastian's Church in Kottiyoor was taken into custody last night and arrested this morning under IPC Section 376 (punishment for rape) and the Protection of Children From Sexual Offences (POCSO) Act, they said.
The alleged offence came to light after the 16-year old girl, a resident of Neendunokki near Kottiyoor, delivered a baby boy at a private hospital in Koothuparamba on February 7.
Based on an information from "ChildLine", police held an inquiry with the girl and her parents.
Mathew, who went absconding meanwhile, was picked up from Chalakkudy in Thrissur district last night and brought here.
Police also found the baby had been left in an orphanage at Vythiri in Wayanad District and shifted it to a government-run orphanage here yesterday.