The priest is accused of raping the teenager in a church complex in Ernakulam nearly five times between January and March, mostly when she came for confession. He has been missing since May 5, when the state High Court rejected his request for bail.
The girl, a Class 10 student, was involved in church activities and had reportedly worked closely with the priest for over a year.
"The church is waiting for directions from the Vatican. We are taking these allegations very seriously as it involves paedophilia," a church spokesperson told NDTV.
The police had then confiscated his passport and therefore believe he may not have fled the country.
A look out notice, or warning at airports and borders, has been issued for the priest. The police are looking for him not just in Kerala, but also in other states including Delhi and Karnataka.
Get Breaking news, live coverage, and Latest News from India and around the world on NDTV.com. Catch all the Live TV action on NDTV 24x7 and NDTV India. Like us on Facebook or follow us on Twitter and Instagram for latest news and live news updates.