"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 that has seen an end to fighting there in return for the enforcement of the Taliban's strict interpretation of sharia, or Islamic law.
Babar said that the government would fulfil its pledge under the peace deal - which covers the Swat valley and the surrounding districts that make up Malakand division - to establish Islamic courts in the area.
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.
"The operation that got under way this morning got under way in an area called Dir, which is adjacent to Swat," Kamal Hyder, Al Jazeera's Pakistan correspondent, said.
"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 today 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.