The girls, all in the age group of 14-15 years, were staying at the orphanage at Muttil in Kalpetta in Wayanad district.
The incident came to light after one of the girls was seen coming out from a nearby shop in suspicious circumstances and was questioned by the orphanage staff, following which a complaint was lodged with the police, they said.
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Any other information about the incident was not known immediately and police said more details would be shared as the probe progresses.
The incident comes close on the heels of a 16-year-old girl being allegedly raped by a church vicar at Kottiyoor in neighbouring Kannur district.
The girl gave birth to a baby boy on February 7 after which the priest was arrested. Seven other accused in the case, five of them nuns and a doctor, are still absconding.
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