"Ball striking wasn't very good today," Ko said after the round.
"I'm hitting my drives really well, but the birdie opportunities I had I was missing quite a few of them. I was putting so much better today until the last few holes."
Ko will remain as world number one even if world number two Ariya Jutanugarn, currently in 18th place, wins the tournament, with projections still giving her a sizeable average points lead atop the Women's World Rankings.
Ko now prepares for the first major of the season, the ANA Inspiration, where she will also be the defending champion.
The news is better for New Zealand's golfers on the PGA Tour, where all three Kiwis playing could make the cut at the Puerto Rico Open.
Tim Wilkinson leads the way, with the left hander firing the best round of the day, a nine-under par 63.
Wilkinson was at two-under through 10 holes but then caught fire, with an eagle followed by five straight birdies to fly 67 spots up the leaderboard into a share of fourth, just one shot off the leaders.
Wilkinson says he played solidly without much reward in his first round, but got on a roll today.
"The back nine, I got - bar one putt on number three - pretty much everything out of it. I wanted it to keep raining, I was making all the birdies in the rain, but I played really well," Wilkinson told the PGA Tour website.
Danny Lee is in a tie for 36th at five-under par after shooting a two-under 70 in his second round, while Steven Alker is in tied 50th at four-under par. Alker has six holes remaining in his round, which was suspended due to darkness.