The airstrike came Friday in Kunar province, which borders Pakistan, the same area where a US transport helicopter was downed late last month, killing 16 troops in the deadliest single blow to American forces since they ousted the Taliban in 2001.
"The president is extremely saddened and disturbed," said Jawed Ludin, President Hamid Karzai's chief of staff. "There is no way ... the killing of civilians can be justified. ... It's the terrorists we are fighting. It's not our people who should suffer."
A government team is on its way to the site to investigate the bombing, a Defense Ministry statement said.
Meanwhile, two members of the US Navy's elite special forces branch -- known as SEALS -- that were missing in Kunar have been found dead, a senior US defense official in Washington said Monday night. Another SEAL was rescued on Saturday and the fate of a fourth was unknown.
The official who confirmed the recovery of the two bodies spoke on condition of anonymity because of the ongoing effort to account for the missing US servicemen in Afghanistan.
The team of SEALS was reported missing on June 28. A rescue effort the same day ended in tragedy when the transport helicopter seeking to extract the team was shot down.
The serviceman rescued on Saturday had taken shelter in a village elder's home before American forces were notified of his location and picked him up, said Kunar provincial Gov. Asadullah Wafa.
Speaking about the US airstrike, Wafa told The Associated Press that an initial strike destroyed a house, and as villagers gathered to look at the damage, a US warplane dropped a second bomb on the same target, killing 17 of them, including three women and children.
He said it was unclear who was killed in the initial attack in the tiny village of Chechal. "Maybe some militants were killed, but I don't know," he said. "The 17 people were killed in the second bombing."
The US military said the attack was carried out "with precision-guided munitions that resulted in the deaths of an unknown number of enemy terrorists and noncombatants."
"The targeted compound was a known operating base for terrorist attacks in Kunar province as well as a base for a medium-level terrorist leader," it said. "Battle damage assessment is currently ongoing."
The statement added US forces "regret the loss of innocent lives and follow stringent rules of engagement specifically to ensure that noncombatants are safeguarded. However, when enemy forces move their families into the locations where they conduct terrorist operations, they put these innocent civilians at risk."
The civilians are the latest victims in an unprecedented spate of violence that has left about 700 people dead and threatened to sabotage three years of progress toward peace. Afghan officials insist the violence will not disrupt landmark legislative elections slated for September.
A purported Taliban spokesman, Mullah Latif Hakimi, claimed last week that militants had captured one of the SEALS team members. He said the "high-ranking American" was caught in the area where the helicopter went down.
Hakimi, who also claimed insurgents shot down the helicopter, often calls news organizations to take responsibility for attacks, and the information frequently proves exaggerated or untrue. His exact tie to the Taliban leadership is unclear.
US officials said they had no evidence indicating any service members had been taken into captivity.
(AP Military Writer Robert Burns contributed to this report from Washington)
