The incident took place on Monday in the city of Mansehra, which is home to several religious schools, said police officer Zulfiqar Jadon.
The seminary instructor, who had been teaching the Quran — Islam's holy book — for several years, and his two companions lured the victim and her friend on the pretext of dropping them off home from college, then raped the girl in a moving car, Jardon said.
The teacher first confessed to the crime, then retracted his statement, saying the two schoolgirls had joined him and his friends on an outing.
The case is unusual since rape cases are rarely prosecuted in Pakistan and women who complain are often stigmatized. Circumstances are even more difficult if a perpetrator is a religious leader or a respected seminary instructor whom the victim would be afraid to report.
The suspects were brought before a court later Wednesday, which allows the police to hold them for four more days while they are being investigated.
As the hearing was under way, townspeople gathered outside the court and held a protest to denounce the crime.
Mansehra's police chief Khurram Rasheed said the protesters pelted the suspects when they came out with bottles of black ink, stones and tomatoes. Blackening someone is a sign of insult in the Pakistani culture.
The protesters also demanded authorities hang the three in public, Rasheed said.
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