Kaliappan was arrested last night.
He was produced before a local court today which remanded him in 15-day judicial custody, police said.
On Monday, Kaliappan had allegedly taken the two girls, who arrived little early in the morning, to the first floor of the school at Karaikalmedu and attempted to molest them.
However, some passersby caught and thrashed the watchman.
They later informed the school head master and the Chief Educational Officer.