The incident took place at the St Mary Church in the upazila’s Mahalipara area, locals said.
A case was filed against Father Pradeep, 50, on Tuesday night at Tanore Police Station.
Officer-in-Charge Rakibul Hasan said they rescued the victim and brought her to the police station. He said the girl would be sent to Rajshahi Medical College Hospital’s One-Stop Crisis Centre for medical tests.
Locals said the girl went missing on Saturday from near the church where she was cutting grass. Her brother filed a police complaint the next day as she remained missing.
Around Monday noon, it was learnt that the girl was confined in Father Pradeep’s room. The victim’s family members and locals rescued her.
In the evening, a kangaroo court at the church found Pradeep guilty and shifted him to Rajshahi.
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The church authorities kept the girl with the nuns and told the family that she would be returned if they withdraw their police complaint.
The church also offered to bear all expenses of the girl until she turns 18.
On Tuesday, the girl’s brother went to the police station and informed that she had been found but was not handed over to the family yet. He said Father Patrick Gomes and kangaroo court head Kamel Mardi had kept his sister confined.
OC Rakibul and Upazila Nirbahi Officer (UNO) Sushanta Kumar rescued the girl from the church in the evening.
“The accused priest has been absconding since the Monday evening,” the OC said. “We’ll arrest him soon.”