Let's set the record straight: It's not Pakistan's new civilian government that is negotiating the peace deals in the tribal areas that are being linked to an upsurge in Islamic militant attacks on U.S. and NATO-led forces across the border in Afghanistan.

    The deals are being done by the Pakistani army and the powerful military intelligence agency, the Inter-Services Intelligence Directorate, supposedly two of the Bush administration's most stalwart allies against al Qaida, the Taliban and like-minded Islamic militant constructs.

    That's an extremely significant distinction. Yet it's a distinction that seems to be lost on the Bush administration and NATO.

    NATO spokesman James Appurthurai today was quoted by news agencies as saying that the alliance is worried that "the deals being struck between the Pakistani government and extremist groups in the tribal areas" are responsible for a 50 percent surge in attacks last month in eastern Afghanistan.

    The Pentagon, which has reportedly decided to keep a Marine unit longer than planned in Garmser, a poppy-producing backwater in Afghanistan's southern Helmand Province, because of an influx of Taliban fighters, is fingering the new government in Islamabad as well.

     "Whatever the new government in Pakistan decides on, we have to pay a lot of attention to," Adm. Michael Mullen, the chairman of the Joint Chiefs of Staff, told al Jazeera television on April 25. "It's a sovereign country and they have to deal with what they've done inside their borders as they see fit. To do that in a way which jeopardizes the lives of Americans certainly would be of great concern."

    To be sure, the new coalition government does favor a different approach to ending militancy in the Federally Administered Tribal Areas that has caused serious heartburn in Washington and allied capitals. It emphasizes negotiations over a previous policy of Pakistani military assaults and missile attacks by unmanned U.S. drones that while taking out bad guys have inflamed the tribes by killing unknown numbers of civilians and displacing thousands of others. They have also driven new recruits into the arms of the extremists. Indeed, one of the government's coalition partners, the Awami National Party, has been working on a truce with extremists in the Swat Valley.

    But the fact is that the new Pakistan Peoples Party-led coalition is in slow self-destruct, totally consumed in back-stabbing and infighting over the reinstatement of independent-minded judges fired by the former military regime. It's the Pakistani army and the ISI that have been concluding the truces in the FATA after failing dramatically to contain the insurgency even while reaping billions of dollars in U.S. funding.

    In fact, as my colleague Saeed Shah and I reported earlier this month, the military began the negotiations in secret - including with Baitullah Mehsud, the chief suspect in Benazir Bhutto's assassination - before the new coalition government was elected in February. And the terms it has been offering are far more lenient than those favored by the civilians who are supposedly its constitutional superiors.

    The army is allowing the militants to keep their weapons and reportedly has begun reducing the number of its troops in South Waziristan. It took the process further today, releasing detained extremists in exchange for captured soldiers.

    Prime Minister Yousef Raza Gillani, however, has made clear that he favors far tougher terms than the army, including negotiating only with those tribesmen who agree to disarm. He said in a recent op-ed in the Washington Post that he also will "not negotiate with terrorists" - i.e. al Qaida - and "will not cut off our ability to use force" - i.e. maintaining troops in Waziristan - against militants who refuse to renounce violence. Moveover, Gillani favors closer cooperation with the Afghan government of Hamid Karzai.

    Gillani's op-ed was intended to reassure the Bush administration, the Pentagon and NATO that the new government will not enter the same kind of disastrous truces that the military concluded in 2004 and 2006 that allowed the Taliban, Haqqani group fighters and other al Qaida-allied groups to pursue "jihad" on the other side of the Durran Line.

    Yet the Bush administration, the Pentagon and NATO insist on blaming the virtually dysfunctional coalition that Gaillani nominally leads - the shots are really called by Bhutto's widower and PPP boss Asif Ali Zadari - not the Pakistani general staff, for the truces that appear to be allowing the current Taliban upsurge in Afghanistan.

   It's not as if U.S. officials don't know who's doing what.

   "What the army really started out doing was saying, 'Okay, we’ve gone about as far as we can for the moment. Let’s start negotiating just to get through the elections without a big flare up in the tribal areas,' and they carried that moment through to the present negotiations," said a senior Bush administration official, who naturally requested anonymity. "I would say that the new government, if anything, has been skeptical and had a positive influence on the state of the negotiations, which has made them more careful."

    That raises the question of why the Bush administration, the U.S. military and NATO are not fingering the Pakistani military? Perhaps they remain as dependent - or hopeful - as ever on its cooperation, and so they don't want to tick it off? A recent report by the non-partisan Government Accountability Office, the congressional investigative agency, did conclude after all that the White House has no comprehensive strategy for dealing with the threat posed by the terrorist sanctuary in the FATA.

    Or perhaps calling out the military would be tantamount to acknowledging that Pakistan's powerful generals are refusing to bend to the new civilian government and continue to maintain troubling ties to Islamist factions despite what was universally hailed as a successful transition to civilian rule?

    Whatever the reason, one can only imagine that the Pakistani military and its former chief of staff, President Pervez Musharraf, are only too happy to allow civilian government to take the hit for the escalating violence in Afghanistan.

    One deeply alarmed senior Pakistani official told me recently that the FATA peace deals will allow the Pakistani military to maintain its influence with militant groups on both sides of the border while continuing to milk the United States for millions of dollars in counter-insurgency assistance.

    And if and when the truces collapse, he said, it will be the civilian government that will be held responsible.