In the opening minutes, it was the visitors who made all the right noises with centre forward Yuri Nagai finding herself in the circle on a one-on-one situation with Brooke Neal but the Black Sticks sweeper kept her cool to push the ball away.
World No 10 Japan attacked again a minute later but it was Merry who coolly scored at the other end for a 1-0 lead in the fourth minute.
Charlotte Harrison had a great opportunity to extend the lead a minute later at the far post but the superb square-cut delivery went begging all the way past everyone to the sideline.
It was another "oooh" moment three minutes later when Harrison couldn't convert a Flynn cross into the circle.
However, Flynn took the matter into her own hands with a field goal in the ninth minute to make it 2-0 for the Stacey Michelsen-skippered world No 4.
The second quarter was conspicuous in the sides' armwrestle for possession and territory but no one prevailing.
In just the second minute of the third quarter, former skipper Whitelock, defender-cum-attacker, showed why she would be an asset for some much-needed impetus with a solid finish to make it 3-0.
That score remained despite some promising surges from the Kiwis and a fine drizzle kicking in.
The visitors, on the other hand, showed the gulf in world rankings and didn't really look like scoring any goals.
In the final quarter, Japan captain Miyuki Nakagawa pulled one back for the runners-up, 3-1, from a goalmouth melee in the 55th minute and another goal followed not long after, courtesy of Mie Nakashima, but it was too little, too late as the seconds ran out for an equaliser.
In the third-fourth playoffs, Australia beat China 3-1.
Final standings: Canada 8th, South Korea, 7th, India 6th, Ireland 5th, China 4th, Australia 3rd, Japan 2nd, New Zealand champions.
