The Australian takes a one-shot lead into the final round of the €2.2 million event with a chasing pack - including world No.7 Ernie Els - breathing down his neck.
Fraser compiled a composed two-under-par 70 at Pinx Golf Club on the Korean holiday island of Jeju on Saturday (24 April) to reach nine-under 135.
The tournament has been reduced to 54 holes after play was held up for six hours on the first day due to fog.
Northern Ireland's Gareth Maybin returned a second successive 68 to stand one shot back on eight-under.
Also on eight-under are Thailand's Thongchai Jaidee, the defending champion, and Tano Goya of Argentina, who both had Saturday off after completing their second rounds on Friday.
Players had to cope with Jeju's famous blustery conditions once again on Saturday and Fraser was pleased with his effort.
"I played really well," he said. "I made a couple of good birdies towards the end of the round, but it was very tough conditions out there so I think two-under was a pretty good score.
"It was just so gusty. It was windy most of the day but a couple of times it dropped and then came back, so it was hard to judge shots coming into the green."
Fraser's best finish this season was joint 11th at the Omega Dubai Desert Classic. His lone European Tour win came seven years ago at the BMW Russian Open.
On his prospects for the final round, he said: "I've got to go out there, give it my best shot and just keep playing well. If the outcome works in my favour, so be it."
Maybin, who is searching for his first European Tour victory, has dropped just one shot in the first two rounds. "I played pretty solidly," he said. "It was pretty blustery out there, so all in all, I'm very happy just to drop one shot.
"Tee to green I've been solid and when I have missed a green my short game has been pretty good. All in all, I'm looking forward to tomorrow."
Three players were grouped on seven-under including South African superstar Els, who shot a 69 on Saturday. Also on seven-under were Korea's Ted Oh (70) and Brett Rumford of Australia, who completed his second round on Friday.
Oh flew the flag for the home nation and delighted the galleries with a round highlighted by an eagle on the par-five fourth. "I'm happy with 70, but I made a couple of silly mistakes on the back nine, so I'm kind of disappointed that way," he said.
Asked about his plan for the final day the California-based Oh, who has yet to win a title since turning professional 11 years ago, said he would just concentrate on his own game.
"I made a couple of mistakes in the past, so I'm just going to go out tomorrow and play my game. I'm not going to look at the leaderboard that much and try to chase it."
Two players were in joint eighth place on six-under - Singaporean Mardan Mamat and England's Oliver Fisher, who both shot 70.
Six-time European Tour winner Henrik Stenson remains in contention - the Swede returned a 70 to stand four strokes off the pace.
PGA Tour star Anthony Kim fell down the leaderboard with a two-over 74 that dropped him to two-under - seven shots behind Fraser.
The Ballantine's Championship is once again co-sanctioned by the European Tour, Asian Tour and Korea PGA.