Spokesman Zabiullah Mujahid also told AFP that the royal was usually kept out of harm's way during his time in the country.
"There are 49 countries with their powerful military failing in the fight against the mujahideen, and now this prince comes and compares this war with his games, PlayStation or whatever he calls it," Muhajid said.
"This is a serious war, a historic war, resistance for us, for our people.
"But we don't take his comments very seriously, as we have all seen and heard that many foreign soldiers, occupiers who come to Afghanistan, develop some kind of mental problems on their way out."
He added: "We have always wanted to capture or kill this prince, but he was mostly kept inside, safe, and in guarded places underground.
"At one point when our mujahideen attacked the airport, we were aware of his presence there but he was hastily flown away."
Asked if he had killed anyone in Afghanistan, Harry had replied: "Yeah, so lots of people have.
"Take a life to save a life. If there's people trying to do bad stuff to our guys, then we'll take them out of the game."
He added of manning the weapons systems in a two-man cockpit to fire missiles, rockets and 30mm rounds: "It's a joy for me because I'm one of those people who loves playing PlayStation and Xbox, so with my thumbs I like to think I'm probably quite useful."
Prince Harry's wild antics - photo gallery:
Copyright: Rex Features Paul Grover/Rex Features