Besides Tuesday's defeat, the second-seeded All Blacks saw star Sonny Bill Williams leave the game with an injury and he will miss the remainder of the competition, reports Efe.
Japan got off to a quick start, taking the lead in the third minute on Teruya Goto's try, converted by Lomano Lemeki.
New Zealand equalized and then pulled ahead thanks to successful efforts by Scott Curry and Akira Ioane, before and after half-time, respectively.
But with two minutes left in regulation, Japan reclaimed the advantage on a try by Kameli Soejima, followed by Katsuyuki Sakai's conversion.
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