The ministry said in a statement that a "technical failure" apparently caused the helicopter to crash yesterday between the towns of Adrar and Reggan in the Tamanrasset region.
The chief of staff of the Algerian armed forces ordered an investigation into the crash.
The statement did not elaborate on the reason for the mission.
Algeria's security forces sporadically clash with extremists, notably members of Al-Qaida's Algeria-based North Africa branch.
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