"Now we have complete control in this area from where miscreants used to go to Afghanistan, Mohmand, Dir, and Swat," said Major General Athar Abbas, an army spokesman. He said the militants were expelled or killed.
Bajur is part of Pakistan's tribal belt that has become the stronghold of Taliban and Al Qaeda fighters waging an intensifying insurgency on both sides of the border.
The army offensive in Bajur was launched in early August, after government officials declared it a "mega-sanctuary" for militants who had set up a virtual mini-state, complete with Taliban-style courts.
US officials, who worried about record fatalities among their forces in Afghanistan, have praised the operation and said it was helping reduce violence on the Afghan side. But the Americans have not halted missile strikes on suspected militants hide-outs in other parts of Pakistan's wild border region, despite Islamabad's protests that the attacks violate its sovereignty.
The army says it faced stiff resistance near Loi Sam from Taliban militants reinforced by foreign fighters, including some from Afghanistan.
Major General Tariq Khan, who commands a paramilitary force, said it could still take six months to a year to gain complete control of Bajur.
Violence and government restrictions have made it virtually impossible to verify accounts of the fighting. Khan said a total of 1,500 suspected militants had died in the operation since August, along with 73 army soldiers.
The region has been seen as a possible hiding place for Al Qaeda leader Osama bin Laden and his deputy, Ayman al-Zawahri, but Khan said the troops had not picked up their trail.
Khan's count of 95 civilian deaths was the first official estimate of noncombatants killed in the fighting. He didn't say whether they were killed by militants or troops, though officials have acknowledged that artillery and air strikes have heavily damaged many residential areas.
Nearly 200,000 people have fled the fighting, many of them to rough camps in Pakistan and Afghanistan.
Reporters driven to Loi Sam yesterday saw damaged residential compounds, some of them connected by militant tunnels, lining both sides of the road.