A spokesman for NATO forces said they were investigating the allegations.
Three Taliban commanders, including a notorious Al-Qaeda-linked militant leader called Shahpoor, were also killed in the raid, district governor Abdul Zahir said.
The air raid was in support of a ground operation by US-led coalition and Afghan forces in a Taliban-controlled valley in the insurgency-plagued region, Zahir said.
"The civilians were killed in the air raid," he said.
It was not clear if the owner of the targeted house was a member of the Taliban or a civilian, but the Taliban were visiting when the home was attacked, Zahir added.
The Taliban often force villagers to provide them with food and shelter.
Four other children were wounded in the raid, Wahidi said.
Civilian casualties caused by NATO forces are a highly sensitive issue in Afghanistan and are regularly condemned by President Hamid Karzai.