Niger troops supported by air power attacked jihadists who have been using Matari forest in Nigeria as a rear base for attacks in Niger, it said in a bulletin seen on Wednesday.
Around 20 terrorists "were neutralized" and 83 suspected members of Nigeria's Boko Haram group were arrested, it said, and then handed over to the Nigerian authorities, it said.
The operation was carried out from March 13-19 by Nigerien troops in the Multinational Joint Task Force, a seven-year-old four-country force aimed at rolling back jihadism in the Lake Chad region, it said.
Boko Haram launched a bloody campaign in northeastern Nigeria in 2009 that has killed over 40,000 people and displaced around two million from their homes, according to UN figures.
But the group split in 2016, giving birth to a rival faction, the Islamic State West Africa Province (ISWAP), which now dominates in a fratricidal conflict.
The Niger army bulletin said the latest operation aimed at maintaining pressure on ISWAP by attacking its forest lair and cutting off lines of supply.
Three bases, supply dumps and motorbikes were destroyed and weapons were seized, it said.
The latest operation comes on the heels of an operation in southeastern Niger against Boko Haram followers who were reportedly fleeing ISWAP.
Last week, Niger state television said that on March 7 military surveillance spotted a "massive movement of people" along the Kamadougou Yoge River, marking the border between the two countries.
They had left a Boko Haram hideout in Nigeria's Sambisa forest after coming under pressure by ISWAP and were heading towards Lake Chad, it said.
"Around 30 terrorists were neutralized" and 960 other people, most of whom were women and children, were detained, taken to the town of Diffa and handed over to the Nigerian military authorities, it said.
The latest bulletin said 1,121 had been handed over.
The vast Lake Chad region, shared by Nigeria, Niger, Cameroon and Chad, is a notorious redoubt for both Boko Haram and ISWAP, who set up camps on islands in its marshlands.
Niger, one of the poorest countries in the world, is also facing a jihadist insurgency on its southwestern border with Mali.
NIAMEY - Niger's army said its troops had killed around 20 jihadists and arrested 83 others in an operation against militants on its southeastern border with Nigeria.