Khan said troops were searching the area on Friday to track and capture the attackers.
The Khyber region is on the route for lorries carrying supplies for foreign troops in Afghanistan.
Fighters have staged regular attacks in the area in recent months, targeting Nato supply depots. Hundreds of vehicles and containers have been torched.
US and Nato officials say the attacks have little impact on their operations in Afghanistan, but have acknowledged they are investigating alternative ways to deliver supplies.