The attack on Friday night in the border district of Gueskerou is the latest to hit the Diffa region near Lake Chad, which is crisscrossed by fighter groups and traffickers.
“Twelve villagers were killed on Friday at around 8:00pm (19:00 GMT) by Boko Haram elements,” a local elected official told AFP on Saturday.
He said 11 of those killed had been shot but did not give further details.
The Gueskerou area, abutting the Komadougou Yobe river that provides a natural frontier between Niger and Nigeria, has been exposed to years of killings and kidnappings at the hands of the Boko Haram.
In March, two attacks in the area left eight civilians and seven police dead.
Boko Haram, whose name roughly translates to “Western education is forbidden”, has waged an armed campaign in northeast Nigeria since 2009.
The group wants to establish an Islamic state which will follow a strict interpretation of Islamic law.
Some 30,000 people have been killed and more than two million displaced since Boko Haram launched its armed campaign. The fighting has since spilled over to neighbouring Niger, Cameroon and Chad.
The group has repeatedly attacked schools, churches, mosques and markets, but state institutions such as police stations and military facilities have remained its primary targets.
Boko Haram allegedly operates its largest camp in the vast Sambisa forest in Nigeria’s northeast.
Nigerian President Muhammadu Buhari promised to crush Boko Haram during his first term election campaign in 2015.
But his administration has failed to end the 10-year violence, with increasing attacks on strategic towns.