Pakistani forces have killed up to 80 alleged militants near the Afghan border after launching an air strike on a religious school that officials said was being used as an al-Qaeda training camp.

The religious facility – known as a madrassa – was destroyed by helicopter fire in a pre-dawn raid this morning in the village of Chingai near Khar, the main town in the Bajaur tribal region, according to a spokesman for the army.

The raid sparked angry protests in the area as local tribesmen and political leaders denounced the military, insisting that those killed were innocent civilians and not terrorists.

The attack came on the first full day of a five-day visit to Pakistan by the Prince of Wales and Duchess of Cornwall. Security chiefs tonight called off the Prince's controversial visit to a madrassa in the border town of Peshawar over fears for his safety after calls by Islamic leaders for revenge attacks following the airstrike.

The strike is the largest to have taken place for months in the remote region, located in the restive North West Frontier Province, where numerous al-Qaeda and Taleban insurgents have sought sanctuary since being driven out by US-led forces after the September 11 attacks in 2001. Pakistan has sent almost 80,000 troops to the border to hunt out the militants.

The Bajaur area borders Afghanistan’s volatile Kunar province, from where extremist groups are believed to regularly smuggle militants, weapons and supplies across the frontier. In January, Ayman al-Zawahiri, al-Qaeda’s number two, was said to have escaped a US missile attack just a few miles away from today’s military assault.

Witnesses said at least three army helicopters swooped on the madrassa after which a huge explosion was heard. Most of the occupants in the madrassa were asleep although a few had awoken for pre-dawn prayers.

The blast shattered the building, tearing mattresses and scattering Islamic books, including copies of the Quran.

The bodies of 20 people wrapped in sheets were laid on the ground for an impromptu funeral service near the site, attended by thousands of angry local people, some crying and others chanting "Long live Islam."

The death toll was expected to rise as dozens of villagers sifted through the rubble of the building, moving blocks of smashed concrete and mud bricks in an attempt to retrieve mutilated bodies from the wreckage.

"We have not carried out a body count, but information we have received from certain local sources and intelligence sources suggests that there may be up to 80 dead," said Major General Shaukat Sultan, the chief military spokesman.

"We had information about the presence of 70 to 80 miscreants, including some foreigners, who were engaging in militant training in this madrassa and we carried out an operation using gunship helicopters and precision weapons," he said, adding that four or five missiles had been fired at the facility.

Amongst the dead was said to be a local Taleban commander called Maulvi Liaqat, who ran the madrassa and was wanted by the authorities for sheltering insurgents.

Mr Sultan said the madrassa compound was far from any civilian areas and added that no women or children were inside at the time of the attack.

But another cleric, Maulvi Faqir Mohammed, believed to have links with Liaqat, said that those killed were innocent victims and vowed that their deaths would be "avenged". And Siraj ul-Haq, a Cabinet minister from the North West Frontier Province, announced he would resign from the government in protest.

"The government has launched an attack during the night, which is against Islam and the traditions of the area," he said. "They (the victims) were not given any warning. This was an unprovoked attack on a madrassa. They were innocent people."

Zahid Hussain, correspondent for The Times in Islamabad, said that the hostile reaction to today’s events would add to anxieties about ensuring the safety of Prince Charles and the Duchess. "This is one of the largest assaults by the military, with a single raid producing an unusually high death toll," he said.

"The news is spreading and sentiments are running high. It has definitely caused anger and militants may retaliate in some way or another."

The attack came two days after 5,000 pro-Taleban militants gathered in Bajaur for an anti-American rally, in which they proclaimed their support for Osama bin Laden and vowed to continue holy war to enforce Islamic law.

It also came on the day a peace deal was expected to be signed between the military and tribal leaders in the region, along the lines of an agreement signed earlier this year in nearby North Waziristan which was aimed at stopping militants operating in the area and crossing into Afghanistan.

But the army insisted it had given warning to the leaders of the madrassa to close the school, and that militants could not hide behind peace deals.

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