The Los Angeles Times published two of 18 photographs of U.S. soldiers and Afghan police posing with dead bodies or body parts of Afghan suicide bombers.
George Little, acting assistant spokesman for the Defense Department, said U.S. Secretary of Defense Leon Panetta "strongly rejects the conduct depicted in these 2-year-old photographs."
Little notes the Pentagon called on the newspaper not to publish the photographs.
Times Editor Davan Maharaj said the newspaper proceeded to "fulfill our obligation to readers."
Anti-American sentiment in Afghanistan escalated this year after the mishandling of the Koran at a U.S. military base in the country.
The Times notes that the U.S. soldiers depicted in the photographs had been identified.
U.S. Ambassador to Afghanistan Ryan Crocker said in a statement that the embassy condemns the "disrespectful" acts from 2010.
"Such actions are morally repugnant, dishonor the sacrifices of hundreds of thousands of U.S. soldiers and civilians who have served with distinction in Afghanistan and do not represent the core values of the United States or our military," he said.
An investigation is under way.