Wasifullah Wasifi, a spokesman for the governor of Kunar province, said Tuesday's strike was successful in killing the three Taliban commanders who were the targets but it also killed civilians, CNN reported Wednesday.
The NATO-led International Security Assistance Force said it was investigating.
The deaths of civilians during the NATO-led airstrikes have been a source of contention between Afghan and U.S. officials for years, with Afghan leaders saying they represent a lack of respect by the United States.
The number of civilian casualties dropped in 2012 compared to the previous year, the United Nations said.
ISAF officials said they also were looking into accusations seven civilians died as a result of a night raid in Wardak province Sunday in which four insurgents were killed, the Revolutionary Association of the Women of Afghanistan said.
Wardak province spokesman Shahidullah Shahid said ISAF and Afghan forces captured the militant but a gunfight ensued at a mosque.
Four insurgents were dead by the time fighting ended, Shahid said.
When residents came to begin retrieving the dead buried in rubble, something exploded, killing seven civilians, Shahid said.
An ISAF spokesman confirmed that four insurgents were killed and said the reports of civilian casualties were being investigated.
"I am aware of reports that indicate there may have been civilians killed, and ISAF and Afghan officials are assessing the situation to determine the facts," spokesman Jamie Graybeal said.
He said the operation didn't include an airstrike, but coalition troops did find a cache of weapons that they destroyed, causing a large explosion.