The South Korean had shared top spot with Englishmen Adam Gee and Simon Wakefield on Thursday but his rivals both carded one-over rounds of 72 to drop into a tie for third.
Kim, starting at the 10th, had eight successive pars before he birdied the 18th and also the eighth and nine – dropping his solitary shot at the par-three second, took advantage to move to six under as conditions became tougher later in the day.
Darren Fichardt moved into second place after he too carded a 69 while fellow South African Justin Walters and Italian Andrea Perrino had the best rounds of the day, shooting 68s, to lift themselves into joint-seventh.
Defending champion Matthew Zions made the weekend after a 72 left him three over.
Both Simon Thornton and Colm Moriarty also made the cut. Thornton shot a 69 to add to his 71 for a total of 140, but Moriarty had a horrid round of 77 for a 146 total.