The Māori team got the first try of the match thanks to Chris Eves.
A quick off-load to Manawatū player Jason Emery, was an easy setup for another try.
Auckland flanker Sean Polwart scored under the sticks soon after and at 25-nil it looked as if it was just going to go the Māori team's way.
But Japan, to their credit wouldn't go down without a fight. A strong rolling maul produced a penalty try.
The Māori All Blacks had the final say with a kick by Robbie Robinson which resulted in a second try to Emery taking the half-time score to 35-7.
Amanaki Lelei Mafi scored under the posts for Japan's second try.
It soon returned when another Manawatū player, Nehe Milner-Skudder scored in the corner.
Captain Charlie Ngatai and James Lowe both scored, while Japan added one more penalty try.
The final score, 61-21 to the All Blacks.
There is no doubt Japan will be re-evaluating their strategy for their next encounter in Tokyo.