Pakistan's army chief has criticised the US military for making unilateral cross-border raids in the the hunt for al-Qaeda's top leadership, as tensions between the allies reached new heights on the anniversary of the 9/11 attacks on America.

In an unusually tough statement, General Ashfaq Kayani, Chief of Army Staff, said that there was “no agreement or understanding with the coalition forces whereby they are allowed to conduct operations on our side of the border”. Pakistan would defend its sovereignty and territorial integrity “at all costs”, he said.

The statement followed revelations this week that President Bush had approved US special forces incursions into Pakistan in July — without the Pakistani Government's approval — and comments by the Chairman of the US Joint Chiefs of Staff, Admiral Mike Mullen, who told Congress that a new cross-border strategy was needed to wipe out al-Qaeda “safe havens” in Pakistan.

The new low in relations between the US and Pakistan came as Western intelligence assessments concluded that the war against Osama bin Laden's al-Qaeda network is being undermined by the resurgence of the terrorist organisation in Pakistan and its continuing links with the Taleban in Afghanistan.

Seven years on from 9/11 the failure to find bin Laden — combined with increasing awareness that the terrorist group is spreading its influence into North and East Africa and is pressing ahead with trying to develop chemical, biological and radiological devices — is forcing a rethink of how to confront the threat.

The US has had successes in eliminating at least three key al-Qaeda players hiding in Pakistan, by using unmanned Predator spy drones armed with Hellfire missiles and precision-guided bombs. The number of attacks has increased significantly, leading to conflict with the Government in Islamabad because targeting al-Qaeda figures in the mountains of Western Pakistan has led to civilian casualties. Last week a ground attack by US commandos in South Waziristan killed 20 people, including civilians, in the first known incursion by US troops since the 2001 invasion of Afghanistan.

The relationship between the CIA, MI6, MI5 and other Western security agencies with the Pakistan Government and the powerful but quasi-autonomous Pakistani intelligence service is viewed as the most important component in the War on Terror. That relationship, particularly now that Asif Ali Zadari, a new and untested President, has succeeded the former President Musharraf, is under increasing strain.

Western intelligence services remain convinced that the core al-Qaeda hierarchy, living in relative impunity in Pakistani tribal areas, is planning further spectaculars along the lines of the September 11 attacks. Attacks in London and elsewhere have shown that al-Qaeda has the ability to adapt its tactics and learn lessons when plots fail.

Key al-Qaeda operators and planners in Pakistan who have survived the watching eyes and missiles of the American Predators have been behind most of the terrorist attacks in Britain, and the security authorities are fully aware that these individuals have the knowhow and the ingenuity to devise new ways of getting round the counter-measures that are put in place to frustrate the bombers.

Al-Qaeda remains obssessed with using commercial airliners for attacks, but of greatest concern are the signs of its interest in developing chemical, biological and radiological devices. The terrorists have already used lorries packed with explosives and chemicals in attacks in Iraq, and are known to be experimenting with anthrax.

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