The secret war – and the hidden lair of the Taliban

Patrick Cockburn investigates the insurgents' mountain hideaway – and a little-known conflict that has killed thousands

The Pakistani army has fought successfully to control mountainous frontier areas once ruled by the Pakistani Taliban, but it remains reluctant to attack the cross-border safe havens of the Afghan Taliban despite American pressure.

Pakistani soldiers in Bajaur district on the Afghan frontier are eager to demonstrate what they have already achieved, showing off captured tunnels dug into the hillside by the local Taliban to protect their fighters against air and artillery attack. On display are some rockets and shells and a broken sign put up outside a building serving as a court house in the last days of Taliban rule reading: "Don't bring any more cases."

In Bajaur, a heavily populated area of mountains and well-watered terraces and valleys, the Pakistani army is once more very much in charge. Col Nauman Saeed, commander of the 3,500-strong Bajaur Scouts, said: "I want to end the misconception that our frontier areas are the most ungovernable in the world."

Even so the Pakistani army is taking no chances. I travelled by helicopter from Islamabad to Khar, the small town which is the district capital, to avoid a 10-hour road trip through at least three mountain ranges. As we drove half a dozen miles along the dusty road from Col Saeed's headquarters, with its neat lawns and beds of roses, to the tunnels and caves where the local Taliban formerly had their headquarters, there was a soldier on guard every few hundred yards. The soldiers did not look as if they expected to be shot at, and the fields around Khar are green with young crops, but there is little traffic on the road and half the shops look closed.

Bajaur may be pacified, but at least a third of Pakistan's half-million strong army is now deployed in the Federally Administered Tribal Areas (FATA) of which it is part. Urged on by the US, the Pakistani military have taken back areas once held by the Pakistani Taliban all along the border, but it is reluctant to enter those like North Waziristan which the Americans see as a crucial base of the Afghan Taliban.

The Pakistani army's campaign in FATA has been largely successful so far. The price has been high in terms of refugees, ruined villages and casualties. In Bajaur the army lost 150 dead and 637 wounded, while several thousand insurgents are claimed dead.

There was little sign of battle damage on Khar, but Col Saeed said that 12 villages totally destroyed in fighting over the last two years have not been rebuilt. Some 70,000 people out of a population of 1.2 million in Bajaur are still refugees, along with a million others from the rest of Pakistan's North West Frontier province.

Many people have died and are still dying in this vicious and little-reported war where it is difficult to get details even when there are many dead. For instance last Saturday some 75 villagers were killed in an air strike by Pakistani jets in the Khyber district of FATA. The army at first said they were Islamic militants, but later admitted that there had been a blunder and victims were being compensated.

Two days after this attack Pakistani officials said that four people had been killed by an American drone hitting a vehicle in North Waziristan. A local resident claimed that in reality 13 civilians, including two children, had died in the explosion.

It may be that local inhabitants are glad to see the back of the Taliban. Officers point out a dry river bed near Khar where people were assembled to watch public executions. But at the same time the area remains very much under military occupation, with frequent checkpoints and fortified outposts. The Bajaur Scouts are recruited from local tribes, but there is also an army brigade in the district.

It is hazardous to draw too many conclusions from an official tour such as the one I was on in Bajaur. There is so much one does not see. But it is impossible for foreign journalists to visit the area without official permission and protection.

Just how necessary this protection is was demonstrated a few hours after I had left Khar when gunmen burst into the house of a local journalist called Imran and shot and badly wounded him and his sister. A press report recalled that Imran's father had been murdered when covering insurgent activities in an earlier incident.

Officially Pakistan decries the use of the American drones, but a senior security official confirmed that the drones rely on information supplied by local agents of Pakistan's ISI intelligence service. Without such intelligence the US officers directing the drones, which are launched from inside Pakistan, would not know who or what to target. Some 73 ISI agents have been killed setting up these intelligence networks. Several of them have been seen on video being ritually beheaded by the Taliban.

The Pakistan army's public denunciation of and private collaboration with the drone attacks is one example of its ambivalent relationship with the US. In American eyes it is reluctant to act against Afghan Taliban safe havens along the border in the same way as it did against their Pakistani equivalents. To many Pakistani soldiers this would be a very different type of war.

Col Saeed says he calls the local Islamic militants "miscreants" who have no aim other than to win power and do not deserve the name of Taliban. He has a much higher opinion of the Taliban fighters in Afghanistan and has his own explanation as to why the US forces in Kunar, the Afghan province across the border from Bajaur, have so little success. "They don't have the legitimacy we do," he says.

He believes that the Afghan Taliban become insurgents and are motivated because they are members of the Pashtun community which has been marginalised. His analysis is confirmed by many American officials on the ground. The strength of the Pakistan Taliban was probably always exaggerated in the West. They were never more than a powerful irritant rather than a real threat to the Pakistani state even when they took over the Swat Valley. Their open bloodthirstiness, demonstrated on videos of the public lashing of women, isolated them politically.

Peace has not returned to FATA. Local papers carry stories down-column of suspected Islamic militants' houses being burned, refugees in flight or returning, a girls' school destroyed by insurgents and many killed by American drone attacks. The army is in control, but it is not clear what would happen if it left. It may find it more difficult to get out of FATA than it was to get in.

Frontier area in numbers

70,000 people Out of population of 1.2 million in Bajaur are refugees.

150 pakistan soldiers killed by insurgents in Bajaur.

75 civilians killed in Pakistan air strike in Khyber last Saturday.

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