It says "hundreds of assailants" attacked a military post in the south-eastern town of Bosso, on the Nigerian border, on Friday night.
A counter-attack on Saturday morning allowed government troops to retake all positions in Bosso, the ministry says.
It says there were several dead and injured "on the enemy`s side".
Boko Haram has not commented on the Nigerien defence ministry`s statement.
The Islamist group is based in Nigeria but is being tackled by a multinational force, including soldiers from Niger.
Niger`s President Mahamadou Issoufou has been praised in the West for rallying neighbouring countries to fight Boko Haram.
In March, six soldiers from Niger`s army were killed in a Boko Haram ambush in the south-east.
Boko Haram attack kills 32 in Niger
05 June 2016
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Thirty Nigerien troops and two Nigerian soldiers have been killed in clashes with Boko Haram militants in Niger, the country`s defence ministry says.
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