"Two horrific tragedies happened in the communities of Libiri and Kokorou, criminals cornered by constant operations by defence and security forces launched attacks on defenceless civilian populations," the defence ministry said in a statement.
The "barbaric acts" saw 21 people killed in Libiri and 18 in Kokorou, including children, the ministry said.
The operations took place from December 12 to 14, the statement said without detailing when the attacks happened.
The communities are located in the Tera border region, an area teeming with fighters which has been subjected to particularly bloody jihadist attacks in recent days.
The frontier lands between Niger, Mali and Burkina Faso have long been a hideout for jihadists linked to the Islamic State group and Al-Qaeda, who have waged an insurgent war against the government.
One of the latest attacks saw gunmen kill 21 civilians in an assault on a goods convoy, local sources told AFP on December 7.
On Wednesday, both the BBC and RFI reported that jihadists had killed 90 soldiers and over 40 civilians in Tera's Chatoumane.
Niger's junta dismissed reports of the attack and deaths as "baseless assertions" and a "campaign of intoxication".
Although AFP was unable to verify those numbers from an independent local source, a Western security source told AFP that 90 to 100 people died in Tuesday's attack.
The military government suspended BBC radio for three months following its report, the latest in a slew of Western media to be sanctioned by the junta since it seized power in a July 2023 coup.
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