The storming of the Red Mosque in the centre of Islamabad may be the deciding factor in the survival in office of President Pervez Musharraf. Already dozens have been killed in the fighting between Islamist militants in the mosque and Pakistani security forces.

If the siege ends in a bloodbath, with many women and children among those killed, the resulting uproar could trigger a general uprising among the tribal and religious groups opposed to the Pakistani leader.

General Musharraf is clearly hoping that most Pakistanis will, however, blame the militants for the bloodshed. Indeed, one reason why he has waited so long before ordering in the soldiers is to show Pakistanis and the outside world that it is the extremists who are deliberately provoking the showdown and are actively seeking “martyrdom”, as their leader has insisted.

Most people in Islamabad have blamed the President for not taking tougher action earlier. They have been shocked and angered by the militants’ violent attempts over the past six months to impose sharia on the capital and the forays by armed students to attack music shops, kidnap women alleged to be prostitutes and target anything seen as “unIslamic”. The Government’s failure to act until now has been portrayed as weakness — despite Musharraf’s insistence that he was seeking to avoid bloodshed.

The security forces have clearly been ordered to avoid confrontation and have repeatedly held back after strafing the campus of the mosque and the adjacent seminary to allow some of the students to surrender and to offer further negotiations. They also hoped that the cutting off of food, water and electricity and the ignominious capture of the firebrand chief cleric as he was attempting to escape in a burka would force an end to the siege.

The military showdown, however, is taking place in the centre of the capital, and General Musharraf’s enemies are sure to exploit it to turn opinion against him. Already the religious conservatives in the vast North West Frontier Province, who have close links with the mosque, are in uproar.

A separate rebellion against central authority is going on in North and South Waziristan, where al-Qaeda’s leadership has found haven. In Baluchistan there has been an uprising against Islamabad by separatists who want greater control of the income from their energy resources. In big cities such as Karachi fighting is endemic between local people and those immigrants from India after Partition, as well as violent attacks and the firebombing of each others’ mosques by Sunni and Shia extremists.

General Musharraf has also added to his troubles by suspending the former Chief Justice, and this has alienated not only the judiciary and civil service, but large sections of the middle class, who have joined demonstrations against his proposal to run again for President while remaining head of the Army.

With his back to the wall politically, General Musharraf has only two alternatives: the imposition of martial law or a deal with the political establishment that would inevitably curb his powers.

He is now negotiating in secret for a return to Pakistan of Benazir Bhutto, the exiled former Prime Minister, against whom all corruption charges would be dropped. Analysts suggest that if she becomes Prime Minister again, she will quickly move to limit the near-dictatorial powers enjoyed by the President.

General Musharraf is gambling that a showdown with Islamist extremists would re-establish his authority. The Army has certainly been itching for a chance to take on the militants, and the confrontation is intended to send a strong message also to ISI, Pakistan’s powerful intelligence service, which is said to be infiltrated by Islamists and has been ambivalent in its role to neutralise Taleban-style militants.

Everything depends on the outcome of the battle at the mosque. For General Musharraf, the stakes could not be higher.

Times Recommends

• Google to digitise Iraqi artefacts
• Renault angers parents by naming new car Zoé
• Analysis: most lawless part of Philippines