Police said Natarajan was arrested last night under the Protection of Children from Sexual Offences Act, 2012 which was invoked for the first time in the district.
There are 79 visually challenged students, including 18 girls, studying in the school.
The eighth standard girl had alleged that Natarajan, handling the carpentry class, had sexually harassed her.
He is the only one who is not blind among seven teachers, police said, adding that he has been remanded in 15 days judicial custody.
Natarajan, however, has denied the allegations, saying the other teachers had forced the girl to give a complaint against him as they were jealous of him.
