The six victims died from gunshot wounds or being burned alive, the ministry said. Another seven people were wounded in the attack and have been evacuated.
The militants torched about 10 homes, the market and some cattle and stole two vehicles, the ministry said.
A teacher in Bosso, 4 km (2.5 miles) from Yebi, said the attackers were young men who arrived on foot, horseback and camel. They filled up two pick-up trucks with food, he added.
Mamadou Bako, Bosso’s mayor, said the death toll could rise because security forces were searching through the rubble of burned homes.
Niger’s southern region of Diffa, which houses many refugees and internally displaced people who have sought to evade Boko Haram violence elsewhere, has been targeted numerous times in attacks blamed on the militants.
The attack took place one day after the military announced the liberation of 97 girls and women from the Islamist group and three days after the rescue of a teenager who was among more than 200 schoolgirls kidnapped from Chibok, northeast Nigeria, two years ago.
The group, headquartered across the border in northeastern Nigeria, seeks to carve out an emirate and impose a strict interpretation of Islamic law. (Courtesy Reuters)