The country's Education Ministry estimates around 5,000 students left school since rebels declared autonomy for northern Mali following a military coup in March.
Opposition generals ousted President Amadou Amani Toure in March, saying he was unable to handle northern militants. A liberation movement has sought an autonomous state in the north, while the Islamic group Ansar Dine, an alleged al-Qaida affiliate, is seeking to apply Shariah law across the country.
"They have introduced their own program and new subjects like Islamic education, or collective prayers that they themselves conduct," Boubacar Sissoko, a schoolmaster in Timbuktu, told the United Nations' humanitarian news service IRIN.
The Economic Community of West African States said it was considering sending troops into Mali under a U.N. resolution to address what it said were "flagrant violations of human rights" in the wake of the coup.
Some rebel leaders in the north met with ECOWAS authorities last weekend.