Newly-appointed leader Hamid Karzai summoned senior US officials, including the US commander of coalition forces in Afghanistan, and "strongly advised them of the grave concern" at the incident.
As many as 40 people may have been killed and 100 injured in Monday's bombardment of a wedding party in the central province of Uruzgan.
The Pentagon has said that preliminary information suggests cannon fire from a coalition warplane may have caused the casualties.
This is the first time the Afghan authorities have condemned a US friendly fire incident, despite several other incidents in which civilians or Afghan soldiers have been hit.
On Tuesday, a US convoy came under fire outside Kandahar and one soldier was wounded in the foot, a US military spokesman said.
Colonel Roger King said Afghans travelling with soldiers returned fire.
The soldiers were returning from a hospital visit to some of those injured in Monday's friendly fire incident.
Campaign to go on
At the meeting with US officials, Mr Karzai demanded that coalition forces "take all necessary measures to ensure that military activities to capture terrorist groups do not harm Afghan civilians".
Foreign minister Abdullah Abdullah told reporters: "This situation has to come to an end. Mistakes can take place, human errors are possible, but our people should be assured that every measure was taken to avoid such incidents".
"There is no explanation that in a country where people have suffered so much under al-Qaeda and the Taleban, they continue to suffer as the result of the campaign against al-Qaeda," he said.
But he said the coalition operation against remaining al-Qaeda and Taleban forces in the country had to continue.
'Attempt to engage'
The US military has denied reports that it attacked the wedding party after mistaking celebratory gunfire for an anti-aircraft attack.
A US military spokesman in Afghanistan, Colonel Roger King, said American aircrews in the area believed the firing was not random but was tracking their course and making a sustained effort to engage them.
He said: "I don't know what was going on in this village, except there were people shooting at coalition forces with heavy calibre machine guns."
US and Afghan officials are on their way to Dehrawad, 400 kilometres (250 miles) south-west of Kabul, to investigate what happened.
US Defence Secretary Donald Rumsfeld has urged caution until results from that investigation are known.
"It's really a mistake for us to make judgments about what took place when we know we don't know," he said at a news conference.
The Pentagon said other villages had also been hit during a two-day campaign against fighters of Osama Bin Laden's al-Qaeda network and the former Taleban regime.
US defence officials said a stray B52 bomb - which had initially been blamed for the accident - had in fact landed in an unpopulated area.
Afghan anger
The Afghan foreign minister said four separate villages had come under attack.
In the bombardment, which lasted quarter of an hour, all 25 members of one family were killed, he said.
The Americans and the Afghans are reported to have differing accounts of what happened, although it is not clear on which points they disagree.
Many of the victims were taken to the nearest surgical hospital, several hours' drive away over rugged terrain in Kandahar.
Medical staff there said they had treated shrapnel wounds and other injuries.
Afghans have reacted angrily to the news of civilian casualties.
Abdul Wadood, a resident of Kabul, said: "It's our tradition to shoot guns a weddings - it doesn't mean we're al-Qaeda".
Newspaper kiosk worker Hafizullah said: "We're very upset at what has happened.
"America must not do it again, killing innocent people in the name of the war against al-Qaeda."