The girls were on their way to the Mirwais Nika high school for girls in Kandahar when two men on motorbikes stopped near the group and sprayed acid in their faces with toy water pistols.
The girls are being treated in a local hospital. Doctors are working to save the sight of three girls, who have suffered serious facial burns.
The republic's interior ministry said it had arrested two men in connection with the attack.
Afghani officials blame Taliban militants, who barred girls from going to school when the group was in power from 1996 to 2001.
"This barbaric act... defying all the Islamic values of the Afghan state, has revealed the true nature of those who call themselves fighters for Islam," the presidential administration said in a statement.
With the growing presence of the Taliban in recent years, hundreds of schools have been attacked in Afghanistan and dozens of teachers and students killed.
