Bajur is part of Pakistan's tribal belt that has become the refuge of Taliban and al-Qaida fighters waging an intensifying insurgency on both sides of the frontier.
Pakistan's army launched an offensive in Bajur in early August, saying the region had become a "mega-sanctuary" for militants who had set up a virtual mini-state.
Commanders had reported stiff resistance near Loi Sam, which sits on a key road, from local Taliban militants reinforced by foreign fighters including some from Afghanistan.
Khan said troops had now overrun the area and were in "complete control" of the town. Eleven tribal militias had joined the government side in the region, he said.
Still, he forecast that it could take between six months and a year before authorities had gained complete control of Bajur.
The general was speaking to reporters escorted to Bajur by the military. Insecurity and government restrictions have made it virtually impossible to verify accounts of the fighting.
Khan said a total of 1,500 suspected militants and 73 troops had died in the operation so far.
The army has acknowledged that residential areas have been badly damaged from fighting and its use of artillery and airstrikes, but has provided no figure for civilian casualties.