There has been intense fighting since Saturday night around the town of Mir Ali, and nearly 200 people had been killed before Tuesday's air assault.
Thousands of families were getting out of the town of 50,000 and outlying villages, making their way on foot, in tractor trailers and cars.
Major-General Waheed Arshad, the military spokesman, said air strikes earlier destroyed most houses around Essori, a village near Mir Ali where most of the fighting was concentrated.
The military had put the death toll from the three days of fighting at 150 fighters, and 45 soldiers.
Residents of Mir Ali said that most people had abandoned their homes after more than 50 houses were damaged.
Faridullah Khan, a local tribesman, said: "Our homes have been damaged severely, most of the families have migrated to relatives' homes in neighbouring towns."
Town 'sealed off'
Witnesses said that that troops had sealed off the town after the fighting started.
"Pakistan needs a military leader who can control both civil and possible military extremism"
Creative_person01, Islamabad, Pakistan
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Malik Iqbal Khan, a tribal elder, told said that residents had used mosque loudspeakers to urge the military not to fire at their homes.
Residents said that four civilians, including three women, had been killed in the fighting, but there was no independent confirmation of this.
On Monday, Major-General Arshad had said: "The clashes broke out after militants set off IEDs [improvised explosive devices] and conducted ambushes on the security forces."
Many Taliban and al-Qaeda members who fled to the region after US-led forces drove them out of Afghanistan in late 2001 have found support in the tribal areas.
"The army is fighting well-trained militants. There are linkages with Afghanistan. Many of them are getting money and weapons from across the border," Arshad said.
Peace deal scrapped
There has been a rise in fighting since July when tribal groups in the semi-autonomous region scrapped a peace deal with under which they would have taken greater responsibility for security in return for a withdrawal of Pakistani government forces.
|"There are linkages with Afghanistan. Many of |
them are getting money and weapons from across the border"
Major-General Waheed Arshad,
Pakistan military spokesman
Nearly 300 people have been killed in attacks, mostly suicide bombings, since army commandos stormed a mosque and religious school in Islamabad, Pakistan's capital, the same month.
In neighbouring South Waziristan, pro-Taliban fighters have been holding more than 200 Pakistani soldiers since capturing them in late August. They are demanding an end to all military operations in the tribal areas bordering Afghanistan.
Kamal Matinuddin, a retired lieutenant-general in the Pakistan army, told Al Jazeera that fighters have been causing "a lot trouble for the army" in the region because of its lack of control over the area.
"There is almost a civil war-like situation in the tribal areas," he said. "It is very difficult for the army to move because their convoys are being ambushed, and so it is a very difficult operation the army has taken upon itself."
General Pervez Musharraf, the president who is waiting for the supreme court to rule on the legality of his controversial re-election on Saturday, has said "terrorism" is one of the biggest challenges to the country.
But the conflict has reinforced opposition among many Pakistanis, mainly in the conservative northwest, to Musharraf over his support for the US's so-called "war on terror".