The Stingrays were reduced to 12 men late in the first half when Tahi Baggaley was sent off for punching.
Despite the setback, they had the class to ease to a comfortable win and remain unbeaten in the premiership after two rounds.
The Whalers will need to work on their defence. They were exposed across the park despite having an extra man in the line for the majority of the game.
Coach David Reedy said his side were not accurate enough and struggled to match their opponents’ intensity.
"We got on the back foot from the start", he said.
"They got their confidence up and just kind of kept the energy going.
"Their intensity is something that we’re not used to and are still trying to develop down here."
The Whalers got off to a poooor start with four Os.
They threw a wayward pass into touch off their first set then gave up a penalty.
The Stingrays converted the early gift.
Dowie made an angled run to the line and scored.
The Whalers responded quickly, though. Intercept king Jordan McEntee-Walters picked off a pass and scampered up field.
Counties scrambled, but prop Cameron Brown rumbled over a few tackles later.
The visitors were getting plenty of traction down the left and Arthur Crichton barrelled over from close range.
The Aucklanders should have scored again moments later but knocked the ball on in the in-goal area.
It mattered not a jot. Some weak defence saw Jamie Price skip by a couple of ineffectual tackles and add to the growing tally.
Midway through the half, it was obvious the Whalers were facing some significant defensive challenges.
But in a moment of utter madness, Baggaley was sent off after he connected with a punch on Otago prop Mika Mafi, who left the field with blood gushing from his face.
The Whalers added a penalty in the last act of the half to cut the deficit to 16-8.
Some more ill-discipline from the visitors piggybacked the Whalers up the field and winger Saimone Samate-Palu crunched his way through the last defenders to score in the corner.
But that was as close as the game got.
Counties struck right back. Despite being down a man, they outflanked Otago.
Winger Walter Fifita did the honours and Dowie crossed again shortly after.
The game slipped further away when the Whalers tried to shovel it wide in the shadow of their own posts and the pass was picked off by Toaiti Ramsay.
Tama Apineru made a nice run out of defence to relieve some pressure on the Whalers.
And a mistake from a high kick saw the Whalers nab a consolation try through Troy Anstiss.
But Dowie completed his hat-trick moments later and Crichton banged over a rare field goal to complete the 17-point win.
NZRL premiership
The scores
Counties-Manukau 35
James Dowie 3, Arthur Crichton, Joey Price, Walter Fifita, Toaiti Ramsay tries; Dowie 3 con, Crichton field goal.
Otago Whalers 18
Mika Mafi, Saimone Samate-Pulu, Troy Anstiss tries; Jordan McEntee-Walters 2 con, pen.
Halftime: Counties 16-8.
