The accused has been identified as Gajanan Bhalavi, a probationary teacher with the English medium school.
The parents of the girl, a class IV student, lodged the complaint against him in wee hours today.
Police Inspector N M Pant said, "We have arrested the runaway accused from his hideout in Chatarpur village on a tip off."
Yavatmal SP M. Raj Kumar said after visiting the school they will not spare the accused.
Bhalavi has been booked under sections 354 (A) and 506 of IPC for sexual harassment and punishment for criminal intimidation, respectively and under POSCO Act.
School Committee chairman Prakash Nandurkar said the concerned teacher has been suspended and that the school management will firmly stand behind the child.
Earlier in the day, anxious parents and people from different parts of city gathered at the school as the word spread about the incident.
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