"Operations are ongoing with the support of partners to counter the ambitions of this terrorist group," the ministry added in a statement broadcast on television.
The ministry made no mention of any casualties suffered as a result of the raid.
An official from Diffa, the capital of the southeast, however warned the death toll was "very heavy in the ranks of the Nigerien army," without providing further details.
Niger's President Mahamadou Issoufou called a meeting of the national security council after the Islamists' attack.
Niger, along with Chad, Cameroon and Nigeria, has recently launched a joint offensive to end Boko Haram's six-year insurgency, which has claimed 13,000 lives and caused about 1.5 million people to flee their homes, the AFP report said.