The alleged offence came to light after the girl, a resident of Neendunokki in the district, gave birth to a baby boy at a private hospital in Koothuparamba on February 7.
Based on information from 'ChildLine', an NGO, the police conducted an inquiry into the incident.
The girl, a Class 11 student of the school where the accused, Fr Robin alias Mathew Vadakkancheril, was the manager, had attended classes on February 6, a day before she gave birth to the baby boy, police sources said.
The girl was taken to a hospital after she complained of stomach pain and the doctors found out that she was pregnant.
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She was then taken to a hospital run by the church where she gave birth to the baby boy.
The newborn was shifted to an orphanage without informing its mother, the sources said, adding that the girl was told that she had undergone an appendicitis operation.
To ensure that the culprit's name was not revealed, her family was allegedly forced to name two others, including her father, for sexually exploiting her, the police said.
Robin had attended a public programme on February 25 and left the place the next day, after the police lodged a case against him under section 376, IPC (punishment for rape) and the Protection of Children From Sexual Offences (POCSO) Act.
He was picked up from Chalakkudy in Thrissur district last night and brought here.
The newborn was shifted from an orphanage at Vythiri in Wayanad district to a government-run orphanage here.
Meanwhile, Mananthavady Bishop Jose Porunnedom removed Robin from the office of the vicar of the parish with immediate effect as per the Canon law.
"The suspension and prohibition will remain in force until the accused has undergone the prescribed legal procedures in this regard and declared innocent," it added.
Reacting to the incident, the Syro Malabar Church spokesperson said, "It is an unfortunate incident. The church has suspended him and removed him from all posts.
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