"I had a few issues to deal with today with some of my equipment," said Cooper afterward. "But I like the Taupo track (the venue for the final round) and I'll be aiming to put things right there. It will be all or nothing for me now in Taupo," he said.
And, while Cooper was forced to accept this set-back in his MX1 title defence, there was also more drama to come in the MX2 (250cc) and 125cc classes.
Defending MX2 champion Hamish Harwood continues to lead his class after the weekend but he has now seen his 20-point advantage almost halved, shaved back to 11 points, after his main challenger, Christchurch's Dylan Walsh, launched a blistering attack at Himatangi.
Walsh won all three MX2 class races at Himatangi - with Takaka-raised but Takapuna-based Harwood finishing runner-up each time - no doubt sending shock waves through the Harwood camp, although even runner-up finishes at the final round should still be enough to see Harwood keep his crown.
The 125cc class was probably always going to end in tears for one of the two main protagonists.
Taihape's Hayden Smith and Karaka's Kurtis Lilly had been level in the points standings after the first two rounds of the series, but it was probably never going to end that way after Sunday's three races in this class.
And when Smith finished runner-up in the day's opening 125cc race to Australian Mason Semmens, a rider making his debut appearance in the series, with Lilly forced to accept third place, a change in the standings was already in the wind.
Smith backed that up by winning the next two 125cc races, with Lilly runner-up both times, and so Smith is now alone at the top of the class standings, eight points clear of Lilly.
The series wraps up with the fourth and final round at Taupo in just two weeks' time, on March 25, with all three classes in the balance and a fierce day of racing on the cards.
Leading overall standings after the third round of four in this season's New Zealand Motocross Championships at Himatangi on Sunday:
MX1 class: 1. Dean Ferris (Australia, Yamaha) 196 points; 2. Cody Cooper (Mount Maunganui, Honda) 195; 3. Todd Waters (Australia, Honda) 179; 4. Luke Styke (Australia, KTM) 157; 5. Rhys Carter (Mount Maunganui, Kawasaki) 40.
MX2 class: 1. Hamish Harwood (Takapuna, KTM) 208 points; 2. Dylan Walsh (Christchurch, Yamaha) 197; 3. Ethan Martens (Waitakere, Yamaha) 153; 4. Kaleb Barham (Australia, Husqvarna) 134; 5. Logan Blackburn (Te Puke, KTM) 134.
125cc class: 1. Hayden Smith (Taihape, KTM) 213 points; 2. Kurtis Lilly (Karaka, Husqvarna) 205; 3. Hayden Wilkinson (Nelson, Yamaha) 154; 4. Dan Bell (Levin, KTM) 143; 5. Ryan Gwynn (Kakaramea, Husqvarna) 122.