Troops are now advancing on the militants' main training area in the Damadola district of Bajaur.
Local residents say hundreds of people are fleeing the area to escape the fighting.
Militants have recently re-established themselves in Bajaur after a military offensive drove them out in 2008.
Security forces overran the Sewai area in the Mamund district of Bajaur on Sunday night, a senior official in Bajaur's main town, Khar, told the BBC's Urdu service.
The official said that troops had captured several important heights in the area during Monday's fighting.
The army has been pounding Taliban positions using fighter jets and helicopter gunships.
At least 15 militants and one soldier were reported killed.
In February 2009, the army said Bajaur had been cleared of Taliban militants following a military operation launched in August 2008.
But recently the security situation has been deteriorating.
Correspondents say that numerous attacks over the last six months show the militants still maintain a significant presence in the area.
Close to the Afghan border, Bajaur has long been suspected of being a possible hiding-place of Osama Bin Laden, Ayman al-Zawahiri and other top al-Qaeda leaders.
Pakistan's military has been focusing on a major offensive, launched in October 2008 in the Taliban stronghold of South Waziristan.
But some analysts say that military operation has simply displaced militants to other parts of the tribal belt.