The military action in Lower Dir threatens a truce between the government and anti-government fighters in neighbouring Swat valley.
However, officials maintain that the Swat peace deal holds, despite the operation.
"The peace deal is intact - the government has not revoked the peace deal," Farhatullah Babar, a spokesman for Asif Ali Zardari, Pakistan's president, said.
"At the same time, the government is determined to root out the militants hell-bent on destroying the law and order situation."
The government agreed a deal with the Taliban in Swat in February in return for the enforcement of the Taliban's interpretation of sharia, or Islamic law.
Babar said that the government would fulfil its pledge under the deal - which covers the Swat valley and the surrounding districts that make up Malakand - to establish Islamic courts.
But he said that the government would not permit the fighters to spread their area of influence.
In recent days, fighters from Swat began entering another district, Buner, which lies just 100km from Islamabad, the Pakistani capital.
Later reports suggested that the fighters had begun to pull out after military action was threatened.
Hyder reported on Sunday: "The military moved in, but they have of course been using maximum restraint because they want this peace deal [in Swat] to work.
"We also got reports ... that the military arrested at least five Taliban who were violating the accord - they were toting weapons in an area of Swat."
Critics of Pakistan's deal with fighters in Swat say that it has only emboldened the Taliban, and, in recent days the US has increased pressure on Pakistan to confront fighters on its soil.
General David Petraeus, the head of US central command, said Pakistan's leaders should focus on the looming threat posed by fighters within their borders.
"The most important, most pressing threat to the very existence of their country is the threat posed by the internal extremists and groups such as the Taliban and the syndicated extremists," he said.
Across Pakistan, more than 1,800 people have been killed in a wave of al-Qaeda and Taliban-linked attacks since July 2007.