About 60 children of the home, run by Malarchi Trust at Rettiyarpatti in the district, were shifted to the juvenile home here.
Its owner Prabakaran, two women wardens and Muthuraj, who allegedly sexually assaulted the 11-year-old girl, were arrested and produced before a local court which remanded them to judicial custody for 14 days.
According to police, about 60 children, all of them below 18 barring Muthuraj, were staying in the home. The victim claimed that Muthuraj had on July 17 taken her to the bathroom and raped her.
Later, when she sought medical help following pain, the doctor found that she had been raped and complained to police.
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The girl has been admitted to the government hospital here.
Acting on the doctor's complaint, police and social welfare department visited the orphanage and conducted inquiries and spoke to the children where some other girl inmates said they had been sexually harassed.
During investigations, it was found the orphanage was operating without proper licence and hence sealed, police said adding that it was receiving foreign aid.