Several parents complained after their children told them the teacher directed the boy to turn his back to the the class and then instructed the other students to "look how ugly he is."
The teacher told Italian state TV he was conducting a social experiment.
Italian Education Minister Marco Bussetti condemned the incident in a public school in Foligno, a town in the Umbria region, as "very grave." Bussetti tweeted Thursday that urgent measures would be taken to address it.
Immigration to predominantly white Italy is a relatively recent phenomenon. The anti-migrant League, one of the two parties in government, issues statements associating foreigners with crime.