Gunmen arriving on motorbikes attacked the villages of Intazayene, Bakorat and Wistane on Sunday, shooting "at everything which moved," a local official said.
The official said at least 40 people died, while a security source gave a provisional toll of 60 dead -- a figure that would bring the number of fatalities in the Mali-Niger border region to 159 in just over a week.
The three villages are located in the arid Tahoua region in western Niger, abutting the Tillaberi region in a border region notorious for jihadist attacks.
On 15 March, suspected jihadists killed 66 people in the Tillaberi region, attacking a bus carrying shoppers from the market town of Banibangou, and then raided the village of Darey-Daye, killing inhabitants and torching grain stores.
Also on 15 March, an attack claimed by the Islamic State group (IS) in the so-called "tri-border area" where the frontiers of Niger, Burkina Faso and Mali converge left 33 Malian soldiers dead.
Sahel security challenges
Tackling the insurgency in Niger and the Sahel region is one of the biggest challenges facing the Sahel nation's new president, Mohamed Bazoum.
Bazoum's election was confirmed on Sunday by the constitutional court.
He offered his condolances to the families of the victims of the weekend's attacks.
On January 2, 100 people were killed in attacks on two villages in the Mangaize district of Tillaberi.
The massacre, one of the worst in Niger's history, occurred between two rounds of the country's presidential election.
The world's poorest nation according to the UN's development rankings for 189 countries, Niger has seen nearly half a million people flee their homes in recent years.
Niger is part of a France-backed alliance of countries in the Sahel region known as the G5.
