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It was the national debut for former Southern Dogs goalkeeper Dominic Dixon, but he had a tough night as the Black Sticks were all over the place.
The side had drawn 3-3 in the opening game of the series on Sunday night but was never in the second match of the series.
A solitary Stephen Jenness field goal in the 21st minute for the Black Sticks left the Kiwis trailing 4-1 at half time.
There was no second half revival this time for the New Zealanders, as Japan piled on the pressure, scoring two further goals in the third quarter and a final goal in the fourth to run out a worthy winner.
Turnovers in the midfield and the speed of the Japanese counterattack caught the Black Sticks out repeatedly and the home side was clinical in front of goal. That and a sub-par performance in terms of general skill level left head coach Darren Smith ruing the result.
''That was a tough day at the office. Our level of performance was way down on our usual standards and we could not have played more into Japan's hand,'' Smith said.
''We gave the ball up easily in the midfield, allowing Japan to break at speed, causing our deep defence problems, and we weren't able to contain them. There will need to be a much better reaction in the third game [tonight at 10pm] in Gifu.''