She pulled back a shot with birdie on the 18th but was left with some work to do on the final day if she wished to add to her four career victories on the LPGA Tour.
Even if she fails to make up that ground, the tournament still represents a successful return to golf for Ko. The 17-year-old recently skipped two tournaments as she rested her troublesome wrist, a joint that had been stricken by a cyst caused by over-practising.
Ko underwent specialist treatment in Korea and spent her time away from the course being a normal teenager in Orlando, going to movies and amusement parks with friends.
The Kiwi cut down on her practice sessions and the break appears to have done her some good in Malaysia, equalling her best round as a professional in shooting a bogey-free seven-under on the second day at the $2.6m event.
Ko has shown her ability to match it with the best in the game during an outstanding debut season as a professional. She has already recorded two wins and another top-10 finish today will be her 11th of the season. Currently sitting third in the LPGA Tour's Race to the CME Globe, Ko could be in line for a US$1 million ($1.3m) prize if she emerges triumphant from the season-long points race.