McCaw is struggling with a minor calf injury and Muliaina has a tight hamstring, so the duo join Dan Carter in being rested for the clash against the minnows.
In McCaw's absence, hooker Keven Mealamu will lead the side while Adam Thomson shifts to openside and Victor Vito comes off the bench to start at No.8. Lock Anthony Boric comes in to the squad on the bench
With Israel Dagg (right abdominal strain) also unavailable Isaia Toeava will now start at full-back.
All Blacks coach Graham Henry said: "It's disappointing to have the players unavailable, especially Richie and Mils who were both looking forward to playing against Japan.
"But injuries are something that we all have to deal with and it's great that we have versatility in the squad so Isaia is able to slot in at full-back."
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