Cooper has elevated himself from fourth after round one to now lead the standings, three points better off than Phillips, with Australian KTM rider Kirk Gibbs in third.
The round-one winner in the class, Queenstown Yamaha rider Scott Columb, crashed during practice early in the day and this may explain why he did not dominate as he had in Taranaki. It was a similar story for Wilson in the MX2 (250cc) class and for Natzke in the 125cc class, both riders also scoring hat-tricks on Sunday.
The MX2 class leader after round one, Wilson now leads new No2 rider Hamish Harwood (KTM), of Takaka, by 20 points.
Defending 125cc champion Natzke moved up one position to claim the No1 spot in the class and is 11 points ahead of round-one winner Cohen Chase (Yamaha), of Taupo.
Round three is set for Rotorua with the fourth and final round at Pukekohe on March 15.
-Standings
(After Round 2)
MX1 class: 1. Cody Cooper (Mount Maunganui, Honda) 124 points; 2. John Phillips (Rotorua, Honda) 121; 3. Kirk Gibbs (Australia, KTM) 114; 4. Kade Mosig (Australia, Yamaha) 101.
MX2 class: 1. Jay Wilson (Australia, Yamaha) 140; 2. Hamish Harwood (Takaka, KTM) 120; 3. Micah McGoldrick (Amberley, Honda) 105; 4. Scotty Canham (Rotorua, Kawasaki) 85.
125cc class: 1. Josiah Natzke (Hamilton, KTM) 138; 2. Cohen Chase (Taupo, Yamaha) 127; 3. Ben Broad (Ngatea, KTM) 118; 4. Kurtis Lilly (Karaka, Husqvarna) 104.