The operation, called "You will like us", is taking place in the Barra Area, where security forces say 18 Taliban fighters have been killed in fighting so far.
Kamal Hyder, Al Jazeera's correspondent in the Pakistani capital, Islamabad, said security officials had arrested six people and at least two hideouts and three Taliban strongholds had been destroyed in the operation.
Authorities have claimed that Taliban fighters who escaped from an army operation in South Waziristan may have sought sanctuary in Barra.
Pakistani officials say the spate of recent bloody attacks in Peshawar and surrounding areas, which have killed more than 150 people, were likely to have been co-ordinated from Barra.
Officials on Tuesday also imposed a curfew in Bajaur district, north of Khyber, after deadly clashes with the Taliban.
Authorities imposed an indefinite curfew after clashes in Khar, the main town of Bajaur district on the Afghan border, where US officials say al-Qaeda is plotting attacks on the West.
"Two civilians were also killed and four, including two women, wounded when a mortar shell landed inside a house," Khan said.
Taliban fighters have recently stepped up attacks on security forces and government installations in Bajaur, one of Pakistan's seven semi-autonomous tribal districts.
The violence has surged since Pakistan launched a major offensive in the Taliban bastion of South Waziristan on October 17.
Officials say the aim is to distract the army's attention from South Waziristan.
The continued unrest comes despite a six-month operation in Bajaur, which the army declared a success in February.