They piled on six unanswered tries in a dominant second-half display.
Trailing 17-15 at the break, the Māori All Blacks surged ahead through lock Laghlan McWhannell early in the second spell and never looked back.
Sam Greene briefly narrowed the gap for Japan with a penalty, but from there it was one-way traffic.
Zarn Sullivan, Sam Nock, Jahrome Brown, Kemara Hauiti-Parapara and Kaleb Trask added to the Māori All Blacks’ first-half efforts from Cole Forbes, Gideon Wrampling and Kurt Eklund.
The nine tries in total secured a statement win in their only clash with Japan this year, and avenged a 26-14 loss in one of their two clashes last year.
Japan’s two converted tries from Kazuma Ueda and Greene’s boot gave them a halftime lead, but they faded under pressure as the Māori All Blacks pulled away in the Tokyo heat.
"I thought the team did extremely well," Māori coach Ross Filipo said.
"In the first 20 minutes, we could see a number of areas of our game that were trying to come together.
"There was definitely a little bit of indecision between some of the boys.
"But as time went on, they started to understand each other, and by the end of the game they were operating really cohesively."
Two Highlanders players, winger Jonah Lowe and flanker TK Howden, started for Filipo’s team.
The Māori All Blacks now head home to face Scotland in Whāngarei on Saturday afternoon.
International rugby
The scores
Māori All Blacks 53
Zarn Sullivan, Sam Nock, Jahrome Brown, Laghlan McWhannell, Kemara Hauiti-Parapara, Kaleb Trask, Cole Forbes, Gideon Wrampling, Kurt Eklund tries; Rivez Reihana 4 con
Japan XV 20
Kazuma Ueda 2 tries; Sam Greene 2 con, 2 pen
Halftime: Japan XV 17-15. — APL/NZ Rugby
