Reports said that nearly 200,000 civilians have fled Loi Sam, the town captured by the Pakistani army.
Major-General Tariq Khan, a spokesman for the military, said government forces captured Loi Sam earlier this week "and killed the militants who were hiding there".
Pakistan's tribal regions are considered a stronghold for the Taliban and al-Qaeda.
The army launched its offensive in Bajaur in early August, saying the region had become a "mega-sanctuary" for fighters who had set up a virtual mini-state.
Khan said troops had by Saturday overrun the area and were in "complete control" of the town, though he forecast it could take between six months and a year before authorities could gain complete control of Bajaur.
But some analysts criticised the military move.
"This is not the first time that the military or the Pakistani government has claimed that they have captured an important person or claimed to have attacked and been successful in destroying the sanctuary of the Taliban," Khalid Rahman, the director general of the Institute of Policy Studies in Islamabad, told Al Jazeera.
"Perhaps the whole strategy is not correct ... I am really afraid that this military strategy is going to increase the problem, unless it is accompanied by a genuine, sincere dialogue."
Talks are meanwhile expected to take place in Islamabad on Monday between Pakistani and Afghan political leaders with an aim to end violence in the border regions. Ethnic Pashtun tribal chiefs are also expected to participate.
The meeting, dubbed a Pakistan-Afghanistan "Jirgagai", or mini-jirga, is a follow-up to a grand assembly in Kabul last year in which delegates called for talks with Taliban fighters.
Around 50 political leaders, Pashtun elders and Muslim clerics from both countries will discuss growing violence by al-Qaeda and the Taliban fighters on both sides of their disputed border.
"The two main objectives of the jirgagai are to expedite the ongoing dialogue process with the opposition and monitor implementation of decisions of the (Kabul) jirga," Mohammad Sadiq, a Pakistani foreign ministry spokesman, said.
But critics say the mini-jirga will be little more than a talking shop without the participation of representatives of the Taliban.