He now leads the MX1 class with 217 points from Scotsman Billy MacKenzie (Yamaha) on 180 points.
MacKenzie was third at Pukekohe with Taupo's Brad Groombridge (Suzuki) performing strongly again to finish runner-up and position himself 12 points behind MacKenzie as the series heads to his home track.
In the 125cc class, Te Puke's Logan Blackburn (Yamaha) returned to the podium after a second round crash at Tokoroa dented his title hopes.
Blackburn posted two seconds and third on Sunday and remains third in the championship standings.
Hamilton's Josiah Natzke (KTM) took a clean sweep at Pukekohe and holds a commanding 35-points lead over Atiamuri's Hadleigh Knight (KTM) with Blackburn 11 points back. Tauranga's Ryan Metz (Yamaha) continued his climb and is now fifth.
The MX2 (250cc) class sees Mangakino's Kayne Lamont (Husqvarna) enjoying an even stronger leadership position than Cooper and Natzke.
Lamont won all three races at Pukekohe and leads by 38 points from Aucklander Hamish Dobbyn (KTM). Australian Jay Wilson (Yamaha) is third and while Rotorua's John Phillips, who is Cooper's teammate in the Honda Shop squad, has moved up to fourth place.
In spite of feeling unwell in the lead-up to the weekend, Mt Maunganui's Rhys Carter (Suzuki) produced his best points haul of the series, taking fifth at Pukekohe and moving to seventh in the title chase.
NZ motocross nationals
(After round three of four):
MX1 (450cc): 1 Cody Cooper (Papamoa) Honda, 217pts; 2 Billy MacKenzie (Scotland) Yamaha, 180pts; 3 Brad Groombridge (Taupo) Suzuki, 168pts; 4 Kirk Gibbs (Australia) KTM, 157pts; 5 Michael Phillips (Rotorua) Honda, 125pts.
MX2 (250cc): 1 Kayne Lamont (Mangakino) Husqvarna, 216pts; 2 Hamish Dobbyn (Auckland) KTM, 178pts; 3 Jay Wilson (Australia) Yamaha, 164pts; 4 John Phillips (Rotorua) Honda, 152pts; 5 Scott Columb (Queenstown) Yamaha, 151pts.
125cc 2-stroke: 1 Josiah Natzke (Hamilton) KTM, 214pts; 2 Hadleigh Knight (Atiamuri) KTM, 179pts; 3 Logan Blackburn (Te Puke) Yamaha, 168pts; 4 Beau Yeandle (Morrinsville) Yamaha, 116pts; 5 Ryan Metz (Tauranga) Yamaha 114pts.