The clash took place in the Tillaberi region in the vast and unstable "three borders" zone between Niger, Mali and Burkina Faso. Jihadist insurgents have staged attacks there for years despite the massive deployment of security forces.
The army said it had killed Abdoulaye Souleymane Idouwal, whom it described as "an influential member of the Islamic State", during a raid on Friday.
The army also said that on Thursday nine "terrorists" were killed and 31 arrested in an anti-jihadist operation in the region.
The army claims to have "destroyed the means of movement" of the assailants and "seized (their) means of communication".
Civilians in Tillaberi are frequently targeted by jihadist fighters, which regularly leads to large-scale displacement.
Niger is ruled by military leaders who seized power in a July coup, citing a worsening security situation as justification for the power grab.
The military government is also fighting Boko Haram jihadists and their rivals Islamic State West Africa Province (ISWAP) in other regions.
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