According to the police, the girl gave birth to a baby boy at a private hospital a couple of weeks ago.
In the initial stages, the victim had given a statement that her own father had committed the crime.
The police said the priest had promised money to the girl's father for accepting the paternity of the child. He confessed to the crime on questioning, the police said.
He is also the manager of the school where the minor girl studied.
Father Robin was the vicar of the St Sebastian's Church in Kannur district to which the girl's family was attached. "He was trying to flee to Canada", the officer said, insisting more details could not be revealed as of now.
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Lawmaker P K Sreemathy said she suspected the priest's involvement in human trafficking. The victim, who delivered a baby in a private hospital at Kottiyoor in Kannur, is a Class 11 student.
Hospital administrator Sister Ancy Mathew said the girl complained of stomach pain. The next day, we reported to the municipal authorities about the birth and the marital status of the mother. Childline is a telephone helpline for children in distress.
In a release issued in Kochi, Varghese Vallikkatt, Deputy Secretary General and official spokesperson of the council, said that the church had taken a serious note of the sexual assault case involving the priest.
He was later presented at the additional district sessions court at Thalassery, which remanded him in judicial custody for 14 days.