The former PGA Tour player, who had a five-under par 67 in round two, is now on a three-under par total nine shots back from American Lee Williams.
Hamilton professional Steven Alker also lost ground with a three-over par 75 dropping him almost 20 places to a share of 45th on an even-par total.
Wilkinson, who is 56th on the Nationwide Tour Order of Merit, and Alker, who is 51st, need to finish inside the top 25 on the money list to automatically qualify for the PGA Tour in 2013.
Meanwhile, Masterton amateur Ben Campbell has found some form ahead of the Eisenhower Trophy with a one-under par 71 in round two of the St Andrews Links Trophy in Scotland to be the only Kiwi to make the cut.
Campbell, who carded a one-over par 72 in round one at the New Course to be in a share of 19th place, climbed eight places to tied 11th with his round on the Old Course at the Home of Golf.
He is 14 shots back from the runaway leader Daan Huizing of the Netherlands who now leads by 10 shots.
The 21-year-old Dutchman stretched his lead after the first round with an eight under par 64 which took him to 14-under par for the tournament.
Huizing's round featured nine birdies, at the 2nd, 3rd, 5th, 6th, 8th, 12th, 15th, 17th and 18th holes, and one bogey, at the 10th, as he made the most of the favourable conditions.
The four other Kiwis in the field Vaughan McCall, Blair Riordan, Daniel Pearce and Mathew Perry all missed the cut of the top 31 players and ties.