The civilians from Madjoari died on Wednesday trying to flee a jihadist blockade, said Colonel Hubert Yameogo in a statement, adding that the toll was provisional.
Survivors told AFP by telephone they had been trying to get away from the attackers as food ran out.
"The people were intercepted and executed by the terrorists," one survivor said. "All the dead were men."
The governor of the region said: "Security operations are underway to restore peace".
One of the world's poorest countries, Burkina Faso has been shaken by jihadist raids since 2015, with the movements linked to Al-Qaeda and the Islamic State group.
More than 2,000 people have been killed and 1.8 million displaced.
Last Sunday suspected jihadists killed 11 people in two villages in northern Burkina.
And last Thursday, 11 soldiers and 15 gunmen died in another attack, in the east, the army said.
In January mutinous troops, angered at mounting losses, ousted elected president Roch Marc Christian Kabore.
Lieutenant-Colonel Paul-Henri Sandaogo Damiba took charge making the security crisis his priority.
But after a relative lull in violence, a surge in attacks has claimed well over 200 lives among civilians and security forces.
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