Milner-Skudder injured his hamstring playing against the Crusaders in their final pre-season game last weekend and didn't make the trip to play the Sunwolves in Tokyo.
Also missing is prop Loni Uhila who has a calf injury.
Coach Chris Boyd's 25-man touring squad includes all four of the Hurricanes 2016 All Blacks with captain and hooker Dane Coles, openside Ardie Savea, wing Julian Savea and star first five Beauden Barrett all on the plane to Japan.
