The Afghan government has called for a rethink in the US-led fight against the Taleban and their allies.
US forces search for the Taleban close to the Pakistan border
Seventeen people, including women and children were killed in a US bombing raid in the eastern province of Konar last week, the local governor says.
President Hamid Karzai is "extremely saddened" by the deaths, his spokesman told reporters on Tuesday.
The US military has now confirmed that it has found the bodies of two elite special soldiers missing in the region.
'Our people suffer'
"The president is extremely saddened and distressed to hear the report that recent military operations in Konar by the coalition forces resulted in the death of civilians," Mr Karzai's spokesman, Jawed Ludin, told a press conference in the capital, Kabul.
"We cannot explain to our own people that they should suffer in our fight against terrorism."
He then went on to call for new ways of conducting the US-led fight against insurgents in Afghanistan.
"Together with our coalition partners, the government of Afghanistan would like to emphasise that we do need to rethink some of our strategies, especially those that can produce tragic results like the death of civilians."
Mr Ludin said the government had opened an investigation into the incident.
The US military has said it regrets that civilians were killed in the air strike but maintains that it struck a valid target, and that enemy "terrorists" were among those killed.
The bombing was part of an operation in Konar province in which US forces were attempting to rescue a number of colleagues stranded in inhospitable terrain where they had been under fire from militants.
A US Chinook helicopter was shot down in the operation, with all 16 soldiers on board killed. The Taleban say they brought it down.
It was the heaviest number of deaths US forces have suffered in a single incident in Afghanistan since toppling the Taleban in 2001.
On Tuesday the US military confirmed BBC reports from Monday that it had found the bodies of two of the special forces soldiers it had been trying to rescue.
A Chinook sent to search for the US soldiers was shot down
A terse statement issued in Kabul said: "The whereabouts of one service member remains unknown."
On Sunday the US military said troops had rescued a fourth member of the team.
Recent months have seen an sharp rise in activity by the Taleban and their allies in south-eastern and eastern Afghanistan.
They have vowed to disrupt parliamentary elections due to be held in September.