He also said that security forces had captured more than 300 foreign fighters, mainly from Afghanistan, Uzbekistan and Tajikistan in the operation.
Forty-two army troops and 31 Frontier Corps personnel "embraced martyrdom," in the operation, Khan said.
"But ... the operation could go for several months before the area is completely cleared of fighters," he said.
Major General Athar Abbas, an army spokesman, said: "Now we have complete control in this area from where miscreants used to go to Afghanistan, Mohmand, Dir and Swat.
"Miscreants have been expelled or killed."
Pakistan's army launched an offensive in Bajaur in early August, claiming that the region had become a "mega-sanctuary" for fighters who had set up a "virtual mini-state with Taliban-style courts".
US military officials have praised the operation and said it was helping reduce violence on the Afghan side.
However, there has been no halt to the regular American missile strikes on suspected fighter hide-outs in other parts of Pakistan's border region, despite Islamabad's protests that its American allies are violating its sovereignty.