Midfielder Anita Punt showed she is the drag-flick queen of the New Zealand team when she continued her dominance in the attacking D with a well-executed shot from a penalty corner to make it 2-1.
With under two minutes left in the first 35-minute spell, Sophie Cocks gave the hosts more breathing space for Hager's pep talk in the dugout.
The 19-year-old Cantabrian rifled a shot towards the cage from just inside the D. Japan defender Emi Nishikori lunged to block the shot but the ball ballooned off her stick and landed in the goalmouth like a golfing pitch-wedge approach to the green for a 3-1 lead.
Japan came out strongly early in the second spell but the Kiwis absorbed the raids to yield a penalty corner in the 51st minute when a defender clumsily took out a New Zealand attacker from behind in the D.
The scrambling defence of Japan thwarted a lusty shot from Central Mysticks midfielder Kayla Whitelock (nee Sharland) but the New Zealand captain prevailed two minutes later when she pounced on a loose ball to thunder it past Japan goalkeeper Royko Oie for a 4-1 margin.
With 17 minutes left on the clock, Petrea Webster should have caused Japan more grief but Oie stuck her padded foot out to deny her a goal.
The visitors' grind became harder when Yuri Nagai copped a two-minute sinbin.
New Zealand then took advantage from a deliberate foot foul to score a one-on-one penalty against Oie to make the lead 5-1.
Nakagawa was pivotal in Japan narrowing the gap to 5-2 when Shihori Oikawa caught goalkeeper Bianca Russell on the hop with a cruel deflection.
With just under nine minutes to go, Flynn claimed her second goal in almost similar fashion to Oikawa as the ball whizzed past in a goalmouth melee.
Olivia Merry was unlucky not to get on the scorecard with the keeper's stick between the ball and the Canterbury striker's pile driver.
Flynn said the attack was clinical and although they didn't take all their chances it was a step in the right direction.
"It's always nice to put six away but again there's always room to work on."
At times the hosts were scrappy and on the odd occasion Japan were able to thread a ball almost the entire length of the field to find an unmarked player.
Such lapses will prove costly against Australia in their must-win clash against their archrivals at 3.30pm tomorrow.
Flynn said the Kiwis always love playing against Australia and relish beating them but it would be a traditionally tough challenge.
The Aussies, who hung around long enough to watch the Kiwis last night, earlier edged South Korea 5-3, while tournament favourites Argentina beat China 2-0 with field goals in the 23rd and 27th minutes.