The protesters in Nangarhar province chanted "Death to Bush" and temporarily blocked the region's main highway.
US officials say they launched the raid early Sunday after receiving a tip that militants in Nangarhar were planning suicide attacks in the coming weeks.
A US military officer, Major William Mitchell, says US-led coalition and Afghan forces came under attack as they approached a compound and returned fire, killing four militants.
The officer says a woman and a teenager were killed in the crossfire, and that two children were wounded.
Afghan police say at least five of the dead were civilians.
US officials expressed concern over the loss of civilian lives.
They accused the militants of endangering civilians by hiding among their families.
The incident marked the second time in two weeks that US-led forces have been blamed for civilian casualties in Nangarhar, a key state in the fight against the Taleban.
Last month, US Marines killed 12 people after being attacked by a suicide car bomber.
Over the past year, militants loyal to the Taleban have carried out the highest number of suicide bombings and other attacks in Afghanistan since a US-led invasion drove the Taleban from power 2001.
Information for this story is provided by AP , AFP, and Reuters.