Karzai quoted in a statement released from his office, said almost 30 civilians have been killed in the airstrike and some others were injured.
He urged the coalition forces to refrain from all sorts of military operations where the ordinary civilians are targeted.
The remarks by comes as local officials said Friday that over 30 Taliban militants were killed in the airstrike which was carried out in Ali Sher district.
A local security official speaking on the condition of anonymity said the airstrike was carried out close to Durand Line where a funeral ceremony was organized for the Taliban group members.
The official further added majority of those killed in the air raid had crossed the line from Pakistan to participate in the funeral ceremony of four Taliban insurgents who were killed by Afghan forces on Thursday.
According to the official, a Taliban leader was also among those killed during the gun battle with the Afghan forces.