In a statement, Major Chris Belcher said: "We are saddened at the loss of civilian life.
"It is extremely unfortunate that militants put others' lives in danger by hiding among their families."
Demonstrators blocked a main road near the provincial capital, Jalalabad, with tree branches.
Suicide car bomb
Some also chanted "Death to Karzai", referring to the president, Hamid Karzai, who is seen by some Afghans as too close to his Western allies.
Last month, US marines killed several civilians when they opened fire in Nangahar after their convoy was hit by a suicide car bomb.
The unit was recalled to the United States soon after and an inquiry is under way.
That incident also triggered a large protest.
More than 4,000 people - including 1,000 civilians - died last year in the worst fighting since the Taliban was ousted in 2001.
Fighting is picking up again after the traditional winter lull.