Militant groups in northern Mali, some of which are aligned with al-Qaida, declared autonomy following a coup early this year.
Human Rights Watch said rebel groups Ansar Dine, the Movement for Unity and Jihad in West Africa and al-Qaida in the Islamic Maghreb are suspected of recruiting child soldiers, summary executions and razing internationally protected sites in the region.
Corinne Dufka, a senior researcher on African affairs for the rights group, said Islamic groups in the north have become more repressive as the crisis lingers.
"Stonings, amputations and floggings have become the order of the day in an apparent attempt to force the local population to accept their world view," she said in a statement from Nairobi.
Human Rights Watch said it conducted close to 100 interviews with witnesses and victims of abuses in Mali since July. The group said it was calling on Islamic rebels to halt conscription of child soldiers and comply with international humanitarian law.
Mali's government this week agreed to host a 3,000-troop strong military united backed by the Economic Community of West African states. ECOWAS forces would help a divided country address the insurgency in the north.
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