Four attackers also died in Niger's southeastern region of Diffa and authorities were searching for two more suspects, a security official said.
Niger, Cameroon and Chad have all suffered a spillover of violence from Boko Haram's northern Nigerian strongholds.
Niger has arrested at least 1,100 suspected Boko Haram militants this year and has placed its Diffa region under a state of emergency.
Diffa, which borders Nigeria, has suffered at least 57 attacks since February, statistics published by the United Nations on Friday showed.
At least 150,000 refugees seeking protection from Boko Haram attacks in Nigeria live in Niger's Diffa region.
An 8,700-strong multinational force comprising troops from Niger, Nigeria, Benin, Cameroon and Chad will begin operations against the militants at the end of this month when the rainy season is expected to stop, Chad's President Idriss Deby said recently.
The force is due to receive U.S. support, including training, worth $45 million.