"Targeting civilians and massacre of defenseless people of Afghanistan is an inhumane behavior and is completely against moral values and international criteria," Qashqavi was quoted as saying.
"Unfortunately, these self-centered actions against innocents have repeatedly happened. We strongly condemn this approach," he said.
NATO's deadly air strike against suspected Taliban insurgents in Kunduz province north of Afghanistan early Friday, according to local officials, left over 100 people dead and injured.
The US and NATO commander in Afghanistan General Stanley McChrystal on the assumption of charge in June promised to avoid harming none-combatants.