"School director Jagdish Kumar and teacher Jagat Gurjar were detained late night yesterday and are being interrogated," SP, Sikar, Vineet Kumar Rathore said.
Meanwhile, angered by the incident, locals demanded strict action against the accused and sought cancellation of the school's affiliation.
The victim's parents in their complaint said that the two had been sexually assaulting her after calling her to school on the pretext of extra classes, according to officials at the Ajeetgarh police station.
Following the complaint by the victim's parents, Yadav and Gurjar were booked on charges of gang rape and getting abortion done without a woman's consent, officials said.
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The matter came to light after the teenager's health deteriorated post abortion. The student is currently undergoing treatment at a hospital in Jaipur.
A case was also registered against a doctor and his wife for carrying out illegal abortion and destroying evidence, the police said.
The incident comes at a time when the issue of safety of school children is already in focus following the murder of a 7-year-old student in an upscale Gurgaon school.