Amnesty International said Thursday that holding children with adults, often without access to lawyers or their families, violates international law.
Researchers who visited Mali in June interviewed seven detainees whom they suspect are minors. The Ministry of Justice told Amnesty it would look into the allegations.
The Amnesty report also criticized the conditions for all detainees and documented the deaths of two inmates.
Northern Mali fell under control of armed separatists and then al-Qaida-linked extremists following a military coup in 2012. A French-led intervention last year scattered the extremists, but some continue to sow violence across northern Mali.