The in-charge of the private hospital at Kuthuparamba in the district, where the 16-year-old girl gave birth to a boy on February 17, and two others, besides the nuns, have been booked under non-bailable sections of POCSO Act and Juvenile Justice Act, Peravoor Circle Inspector, Sunilkumar, who is the investigating officer in the case said.
A report has also been submitted to the State Commission for Protection of Child Rights and Kannur district police superintendent against the Chairman and a member of the Child Welfare Committee of Wayanad district for hiding facts in the case, he said.
The report recommends action against them for concealing details of the newborn from the authorities.
Based on a complaint lodged by the victim's mother with the Childline that Fr Robin alias Mathew Vadakkancheril had "sexually exploited" her daughter last year, the vicar was arrested on February 28.
He was also removed from office by church authorities.
The 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.
The 11th standard student was studying in the school in which the accused was also the manager, police said.
Robin had attended a public programme on February 25 and left the place the next day, after police lodged a case against him under IPC section 376 (Rape) and the Protection of Children From Sexual Offences (POCSO) Act.
He was picked up from Chalakkudy in Thrissur district and brought to Kannur.