Lt. Col. Mark Wright said the Bibles printed in the two most common Afghan languages were seized on arrival at Bagram Air Base because U.S. military rules forbid troops from proselytizing.
"The decision was made that it was a 'force protection' measure to throw them away, because, if they did get out, it could be perceived by Afghans that the U.S. government or the U.S. military was trying to convert Muslims," Wright told CNN.
He said military officers considered sending the Bibles back to the church but worried the church might turn around and send them to a different organization in Afghanistan.
The situation came to light recently after al-Jazeera aired a video in which a reporter suggested U.S. troops were being encouraged to spread Christianity.
The military did not identify the church that supplied the Bibles.
Florida bear attack: Black bear mauls woman's face
Texas principal bans speaking Spanish, stirs controversy