As riots over the accidental improper disposal of the Koran led to seven deaths by Wednesday, two senior NATO military officials stressed that it was because of clandestine communications written into the Korans in the first place that a decision was made to have them destroyed by U.S. troops.

Afghan detainees at Bagram Air Base wrote inside Korans as a method for passing messages to fellow detainees, defacing the holy books in a manner considered blasphemous within Islam, the officials said, speaking to Fox News exclusively.

One official stressed that "while this was the reason the books were removed from the library, we sincerely regret that they were not handed over to Afghan religious authorities for proper disposal and removal, which would have been the correct procedure."

A second official said that local religious leaders who came to look at the damaged material as part of an investigation into the incident were "shocked by what they saw." 

Pages of the Korans contained many handwritten messages and in some cases printed notes were found inside the books. This official described the messages as "extremist" in nature.

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The joint Afghan and NATO investigation will include photo evidence of these messages, this official said.

NATO and International Security Assistance Force officials are not excusing themselves for burning the material. Leaders ranging from Secretary of Defense Leon Panetta to Commanding officer in Afghanistan Gen. John Allen and their spokespeople have all acknowledged a serious mistake in judgment.

"This incident was completely unintentional. Material was inadvertently given to troops for burning. The decision to burn this material had nothing to do with it being religious in nature or related to Islam. It was a mistake. It was an error," ISAF spokesman Brigadier Gen. Carsten Jacobson said Wednesday during a briefing with Pentagon reporters.

Nevertheless, Afghans have continued to protest. More demonstrations occurred Wednesday both inside Kabul and outside Bagram Air Base. Jacobson said at one point on Tuesday protesters had to be fired on with rubber bullets to stop them from trying to enter the base. The U.S. embassy in Kabul was also shuttered and a statement released warning Americans to stay away from forming riots.

All this began when Afghan employees working a night shift earlier this week at Bagram Air Base discovered U.S. troops burning religious materials. Jacobson said these locals stopped the burning, then removed some of the burned books and took them off base to show other members of the community.

On Tuesday night, Allen issued a new directive requiring all coalition forces complete a training regiment on the proper handling of religious materials no later than March 3. According to Jacobson, the training will the identification of religious materials, their significance, and proper handling and storage.