Announcing an inquiry, US Gen John R Allen said any "improper disposal" of religious materials was inadvertent.
Reports suggest the books were taken from prisoners after the US uncovered a secret Taliban message system.
Rumours that a Koran had been burnt led to protests outside
the US base at Bagram north of Kabul. One man was hurt when Nato troops
fired rubber bullets.
President Hamid Karzai condemned the reports that the Koran
had been burnt, as did the Taliban who said the incident would hurt the
feelings "of one billion Muslims around the world".
US Defence Secretary Leon Panetta called the incident "inappropriate and deeply unfortunate".