The fight against the Taliban and Al-Qaeda is not the only conflict on the Pakistan-Afghan border, writes Graham Usher in Islamabad On 23 November NATO lent rare praise to Pakistan's counterinsurgency operations on the Afghan border. Our "cooperation with Pakistan is the best it has ever been," said Brigadier-General Richard Blanchette, spokesman for NATO's International Security Assistance Force (ISAF) in Afghanistan. He was referring to army actions in Bajaur, a tribal agency on Pakistan's northwestern edge. Pakistani forces have been waging a ferocious war there that has not only left 1,500 "militants" dead, and 300,000 locals homeless, but reduced cross-border infiltration into Afghanistan by 70 per cent, say NATO commanders. "This operation will help to deny to the enemies of Afghanistan safe havens in Pakistan," said Blanchette. Three days before, the United States Ambassador in Islamabad was summoned to the Foreign Office. Pakistan was protesting against another missile attack inside its territory by a pilotless CIA directed drone: this latest attack killed five people in Bannu, 70 kilometres from the Afghan border. The ambassador said she would convey Pakistani concerns to Washington. Where they fell on deaf ears. On 22 November US missiles killed another five people in North Waziristan, including, say Pakistan security officials, Rashid Rauf, a British citizen of Pakistani origin and alleged brain behind an Al-Qaeda- inspired plot to blow up a transatlantic aircraft in 2006. His was the 21st US attack inside Pakistan in 12 weeks. More than 120 people have been killed, including women and children. None has coordinated with Pakistan, says the army. "A five minute warning is not coordination," snorts an officer. How to explain this incoherence? On the one hand, NATO ladles out praise. On the other, US Special Forces are engaged in a policy of preemption inside Pakistan, driven, admits the officer, by the conviction that any intelligence shared with its Pakistan counterparts will be leaked to the Afghan Taliban. There are two explanations. The first is that the incoherence is a charade. So far from being "unilateral acts of aggression", the Pakistani government has "tacitly" agreed to US strikes within its territory but with the caveat that it will "complain noisily" about them. The army refutes the charge. And so, noisily, does the government. Addressing parliament on 20 November, Prime Minister Youssef Raza Gilani said the US attacks were "intolerable". But his government admits it cannot stop them. Others are less meek. On 23 November the small but influential Jamaat-I-Islami movement warned that it would sabotage NATO's main supply lines in Pakistan and/or "march on Islamabad" if the attacks did not cease. Both calls have resonance, including in the army. The other explanation is that there is a genuine conflict of interests being fought out in the borderlands between the US and Pakistan armies. In Bajaur there is cooperation, but not because the army is combating Taliban and Al-Qaeda's "safe havens". Rather the army is fighting against what it perceives to be an indigenous but anti- Pakistani insurgency fomented in some part by India and the Afghan government, Islamabad's regional rivals. But in North and South Waziristan -- where 20 of the 21 attacks have been targeted -- there is no cooperation. Both are strongholds of the Afghan Taliban, whence attacks against NATO and US forces are planned and launched. They are also areas where the army has peace deals with pro-Pakistan Taliban forces. The US wants the army to take the war to them with the same vigour as it has in Bajaur. "We lack the capacity to do so," says the officer. "Were we to take on every Taliban group along the Pakistan-Afghan border we would lose whatever control we have there." But there's another reason why the army won't combat all shades of the Taliban. It is convinced that Washington's tilt is now in favour of India as the dominant power in South Asia. One sign of this is the Bush administration's recent deal in which India is allowed to engage in nuclear trade despite not being a signatory of the Nuclear Non- proliferation Treaty. The same privilege has not been afforded Islamabad. Another is the perceived increase in Indian influence over US policy in Afghanistan, concretised in the missile strikes. Since 9/11, India has invested $2.1 billion in Afghanistan, helped train its military, reopened four consulates, and, with Iran, is building a road network that when completed will circumvent landlocked Afghanistan's need to use Pakistani ports to the Gulf. As many have noted, this is a mighty commitment to a country that is 99 per cent Muslim, shares no border with India and is probably the most dangerous place on earth to do business. For the army it is the realisation of Pakistan's worst nightmare: the cultivation of an Indian client state on its western border to supplement the immense power Delhi commands on its eastern border. For many in the military -- and not only there -- this pincer is the first move in a plot to dismember Pakistan as a Muslim, nuclear- armed state. "Within the military establishment I think the fear of India is growing," says analyst Ayesha Siddiqa. "And it's a major driver of military policy, especially as India is now allied with America." In such an environment the idea that the army will sever its ties with the Afghan Taliban and other pro-Pakistani Islamic movements is imaginary, no matter how many missiles the CIA pummels into Waziristan. Says an analyst who refused attribution: "The army's view is that any abandonment of the Afghan Taliban will strengthen India and the Afghan government at Pakistan's expense. And it will maintain this stance until the US listens to what the army regards as Pakistan's legitimate regional concerns." American President-elect Barack Obama says he will listen to Pakistan. The new US military commander in the region, David Petraeus, has advocated a more "regional" approach to Afghanistan, one in which Pakistan is deemed a partner rather than a threat. One way both men could lend credence to this new sensitivity would be to use their prestige to end the US strikes inside Pakistan. In Islamabad earlier this month Petraeus made no such pledge. Neither has Obama.