The teacher, surnamed Lu, was detained at Mohei Primary School in Muzhuo Township, in Zhaotong City this week, state-run Xinhua news agency reported.
Police in Muzhuo Township received a report on July 29 from a villager who complained that his daughter had been raped by the teacher.
The case caused public concern through media reports, which said several girls in the school were raped by the teacher.
All of the victims are children who live with relatives while their parents work in the city, known as "left-behind" children.
China has more than 60 million rural children who are left to relatives, usually grandparents.
According to a 2013 report released by the All-China Women's Federation, nearly 3.4 per cent of the children live alone.
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