The Pentagon tried to satisfy some of the military lawyers' concerns by including some protections of Article 3 in the new policy, most notably a ban on inhumane treatment, but refused to embrace the actual Geneva standard in the directive it planned to issue.
The military lawyers, known as judge advocates general, or JAGs, have concluded that they will have to wait for a new administration before mounting another push to link Pentagon policy to the standards of Geneva.
"The JAGs came to the conclusion that this was the best they can get," said one participant familiar with the Defense Department debate who spoke on condition of anonymity because of the protracted controversy. "But it was a massive mistake to have withdrawn from Geneva. By backing away, you weaken the proposition that this is the baseline provision that is binding to all nations."
Derek P. Jinks, an assistant professor at the University of Texas School of Law and the author of a forthcoming book on Geneva called "The Rules of War," said the decision to remove the Geneva reference from the directive showed the administration still intended to push the envelope on interrogation.
"We are walking the line on the prohibition on cruel treatment," Jinks said. "But are we really in search of the boundary between the cruel and the acceptable?"
The military has long applied Article 3 to conflicts -- including civil wars -- using it as a minimum standard of conduct, even during peacekeeping operations. The old version of the U.S. directive on detainees says the military will "comply with the principles, spirit and intent" of the Geneva Convention.
But top Pentagon officials now believe common Article 3 creates an "unintentional sanctuary" that could allow Al Qaeda members to keep information from interrogators.
"As much as possible, the foundation is Common Article 3. That is the foundation," the senior official said, speaking on condition of anonymity because the new policies had not been made public. "But there are certain things unlawful combatants are not entitled to."
Another defense official said that Article 3 prohibitions against "outrages upon personal dignity, in particular humiliating and degrading treatment" could be interpreted as banning well-honed interrogation techniques.
Many intelligence soldiers consider questioning the manhood of male prisoners to be an effective and humane technique. Suggesting to a suspected insurgent that he is "not man enough" to have set an improvised explosive device sometimes elicits a full description of how they emplaced the bomb, soldiers say.