Afghan President Hamid Karzai is to summon the head of US-led coalition forces for a "full explanation" of a raid officials say killed 16 civilians.
Many people were injured in the fighting
Mr Karzai, who is currently abroad, has ordered an investigation into Monday's air attack in the southern province of Kandahar.
He also condemned Taleban fighters saying they had hidden behind civilians using them as "human shields".
The US military says they may have killed up 80 Taleban fighters.
Mr Karzai, who is in the United Arab Emirates, made his comments in a press release issued in Kabul on Tuesday.
President Karzai expressed concern about coalition forces' decision to bomb the Panjwayi district in Kandahar province.
His statement says that "on several occasions in the past, the president had called on the coalition forces to be highly cautious to avoid civilian casualties during their military operations and not to be swayed by terrorists' tactics who use people's homes as a shelter".
The president has "ordered an investigation into the incident and asked to summon, upon his return to Kabul from the UAE visit, the Commander of the Coalition Forces in Afghanistan for a full explanation about the incident," the statement says.
Mr Karzai also condemned what he called the militants' "act of cowardice" by using civilians as human shields.
He called on Afghans "to resist the terrorists and not to allow them to use their homes as a shelter and for other purposes".
The precise number of dead from Monday's attack is not clear.
Afghan officials say 60 Taleban and 16 civilians were killed.
The US military put the number of confirmed Taleban deaths at 20, with possibly another 60 killed.
It said on Monday it was aware of reports of civilian casualties and was investigating them.
There has been a dramatic upsurge in fighting in southern Afghanistan over the past week.
Officials estimate up to 200 rebels have been killed in the region since last Wednesday, in some of the fiercest fighting since the fall of the Taleban in late 2001.
Further violence on Tuesday has left at least 20 people dead in two attacks.