Capt. Joseph Edward Mullins, 34, was transported to hospital with minor injuries after he lost control of the craft during landing.
"Upon landing, the pilot found that he was losing control, a lot it attributed possibly to the weather," said military spokeswoman Capt. Joanna Campbell. "The runway surface conditions were not good and there was water on the runway.
"At that time, the pilot lost control and standard operating procedures dictate that he is to eject himself from the plane."
Campbell said an explosives disposal team finished removing one of the jet's damaged missiles Saturday afternoon.
The Aim-7 Sparrow missile had dislodged during the landing and was found on the runway. It was to be transported back to Cold Lake.
"There was some damage to two missiles on board," Campbell explained. "It was caused by shaking of the missiles during landing."
Campbell stressed that although the missiles were "live," the area around the plane was safe. The incident came just a day after a missile dropped off another jet and landed on a closed golf course driving range. No one was injured.
Both planes were from 4 Wing in Cold Lake, Alta., and had been on their way to Inuvik to monitor Canadian air space during exercises by the Russian air force.
Capt. Paul Umrysh, another fighter pilot who was making the trip to Inuvik, told Global news that Mullins was recovering from the incident.
"The results aren't back yet," said Umrysh. "But it looks like he's going to be just fine. Obviously a little beaten up from punching out. It can be a pretty extreme ride. But as far as we know at this time, he's going to be fine."
Yellowknife's airport was evacuated immediately after the jet landed. It was to reopen Saturday evening, said Campbell.
"It's all in concern to the travelling public," airport official Michel LaFrance told Global news. "This morning we evacuated the terminal building. We've also evacuated Adlair (a neighbouring hangar) and we have closed off the road."
Umrysh said for fighter pilots, dangerous landings can be just another part of the job.
"It has happened before," said Umrysh. "And that is a fact of the business. We're landing at fairly high speeds."
A highway in the immediate vicinity of the airport had also been closed.
" 'Are they training beginners on CF-18s in Yellowknife?' was my first thought," laughed one woman who was evacuated from the airport.
The military is still investigating why the missile fell off the CF-18 in Friday's incident.
Note: Source: The Canadian Press