A crowd of at least 2,000 angry protesters gathered outside the main U.S. military base in Afghanistan Tuesday, following reports that foreign troops inside the facility had improperly disposed of copies of the Quran.

Some of the protesters chanted anti-U.S. slogans, hurled stones, and set small fires outside the Bagram Airbase, north of Kabul, as guards responded with rubber bullets.

The commander of the international coalition, U.S. General John Allen, issued an immediate apology and ordered an investigation into a report that coalition forces “improperly disposed” of a large number of Islamic religious texts, including the Quran.

“I assure you…I promise you…this was not intentional in any way. I offer my sincere apologies for any offense this may have caused, to the President of Afghanistan, the Government of the Islamic Republic of Afghanistan, and most importantly, to the noble people of Afghanistan.”

Allen said NATO is taking steps to make sure that this “does not ever happen again.” He said the texts have been given to religious authorities to be “properly handled.”

Later Tuesday, U.S. Defense Secretary Leon Panetta also apologized for the incident. He said he approved of General Allen's “swift and decisive action” to jointly investigate the incident with the Afghan government.

The circumstances surrounding the alleged desecration are unclear. Unconfirmed reports suggest that NATO troops attempted to dispose of a load of Qurans by setting them on fire, but were stopped by Afghan employees at the base.

Afghan protests against the destruction of the Muslim holy book have turned deadly in recent years. In April 2011, about 20 people were killed during several days of protests across Afghanistan after little-known U.S. pastor Terry Jones burned a Quran at his small Florida church.