Whibley started on the second row about 30 seconds behind the leaders but charged his way forward and had taken the lead just before a lap was completed.
The track deteriorated fast in several sections and, by the second lap, bottlenecks and some deep ruts were providing plenty to keep riders' minds on the job.
Whibley was able to continue to extend his lead but track conditions meant it could disappear at any time with a slip-up on the slick clay or by getting wedged in a rut.
An early pit stop was needed with the thick, heavy dirt causing him to use more fuel than normal.
A little enduro-X section near the pits also kept the spectators and pit crew entertained, with many riders coming undone on the slippery logs.
Auckland's Chris Power had been running in second place when his bike stopped in a deep rut, boiling all the coolant out of his radiator.
At the finish Auckland's Michael Skinner, Whangamata's Jason Davis, Tauranga's Reece Burgess and Whakatane's Peter Smit rounded out the top five behind Whibley.