The accidental deaths happened in a botched retaliation attack after insurgents fired at an American outpost in Kunar province.
The victims, all of whom were boys, were gathering firewood on a mountainside when they were hit.
The deaths elicited anger from Afghans, with dozens protesting in Kunar Wednesday, according to Voice of America.
Petraeus’ apology came hours Afghan president Hamid Karsai condemned the killings as “ruthless.”
Officials are now investigating whether there was a miscommunication between ground control and crews of the attack helicopters, according to media reports.
The incident has further jarred the already rocky standing of NATO with Afghanis. VOA reported that NATO forces killed as many as 64 Afghan civilians in separate attacks in February.