It's the second military attack in three days with reports of civilian deaths.
But the U.S. military blames the claims on militant propaganda, saying its missiles only hit insurgents. A spokesman says the military has repeatedly seen militants falsely claim civilians were killed.
Even so, the American commander of NATO forces in Afghanistan tells The Associated Press that the two reports are being investigated.
President Hamid Karzai had already ordered an investigation into allegations that missiles from U.S. helicopters struck civilians on Friday in eastern Afghanistan.
But the Defense Ministry said today that the attack killed or wounded 20 militants.
The issue of civilian casualties has caused friction between the Afghan government and U.S. and NATO troops. And it's weakened the standing of the Western-backed Karzai in the eyes of the population.