The West African country has been battling an armed uprising by rebel groups, some linked to al-Qaeda and ISIL (ISIS), which controlled large swaths of territory within and waged frequent attacks across the Sahel.
"During operations which made it possible to neutralize several dozen terrorists, the strikes, unfortunately, caused collateral victims within the civilian population," the army said in a statement on Wednesday.
It did not say how many civilians were killed. The victims were hit by projectiles in the zone between Kompienga and Pognoa, near the border with Togo, on Monday, it said.
Togo, which has been contending with the spillover of militancy from Burkina Faso, accidentally killed seven children in an air raid last month near the same border.