General Stanley McChrystal admitted in a videoconference late on Friday that so far many civilians have fallen victim to arbitrary firing from convoys and checkpoints in Afghanistan.
"We have shot an amazing number of people, but to my knowledge, none has ever proven to be a threat," the top general said.
Since assuming power last year, McChrystal has sought to reduce the killing of civilians through tougher rules.
United Nations human rights researchers say the new directives have led to a 28 percent reduction in such casualties. Nevertheless, despite McChrystal's efforts, such indiscriminate shootings have not stopped.
According to military officials at least 30 innocent Afghans have been killed and 80 others wounded in shootings carried out by US-led troops since last summer.
Other tallies put the civilian death toll much higher, as the military estimate does not include shootings carried out by private security firms.
This failure to curb civilian casualties has led to growing resentment among war-weary Afghans, turning them firmly against the occupying Western forces.
The issue has already deeply undermined American and NATO relations with Afghanistan.
More than 121,000 US and NATO troops are currently stationed in Afghanistan under McChrystal's command. The number is set to rise to 150,000 by August.
The almost-9-year-long US-led invasion was allegedly aimed at destroying militancy and arresting top militant leaders including al-Qaeda leader Osama bin laden but to no avail.