Wing-back Storm Roux, who featured in both of the games against the Solomon Islands, was also not considered because of a lower-back injury.
Wing-back Dane Ingham and midfielder Bill Tuiloma come back into the 22-man squad after missing the September window following concerns on their fitness. Midfielder Clayton Lewis was not considered for selection due to him only recently signing with Scunthorpe United.
Michael Woud, the goalkeeper for the Sunderland U-23 side and New Zealand U-20 team, comes in for his first tour with the national team alongside the experience of Stefan Marinovic.
The All Whites have a good record against Japan. Throughout their history they have played them five times and won on three occasions.
The most recent international between New Zealand and Japan was in 2014 in Tokyo where Chris Wood scored twice but the All Whites went down 4-2.
All Whites squad for the Tour of Japan (Club, Country - NZ unless noted, caps and goals)
Goalkeepers
Stefan Marinovic (Vancouver Whitecaps FC, Canada, 21, 0 )
Michael Woud (Sunderland FC, England, 0, 0)
Defenders
Michael Boxall (Minnesota United FC, USA, 28, 0)
Sam Brotherton (Sunderland FC, England, 9, 0)
Kip Colvey (San Jose Earthquakes FC, USA, 12, 0)
Tom Doyle (Wellington Phoenix FC, 7, 0)
Andrew Durante (Wellington Phoenix FC, 21, 0)
Dane Ingham (Brisbane Roar FC, Australia, 4, 0)
Winston Reid (West Ham United FC, England, 21, 1)
Themi Tzimopoulos (PAS Giannina FC, Greece, 13, 1)
Deklan Wynne (Vancouver Whitecaps FC, Canada, 13, 0)
Midfielders
Michael McGlinchey (Wellington Phoenix FC, 49, 5)
James Musa (Sporting Kansas City FC, USA 3, 0)
Moses Dyer (Eastern Suburbs AFC, 10, 0)
Marco Rojas (SC Heerenveen FC, Netherlands, 37, 5)
Bill Tuiloma (Portland Timbers FC, USA, 21, 0)
Ryan Thomas (PEC Zwolle FC, Netherlands, 15, 3)
Forwards
Monty Patterson (Ipswich Town FC, England, 15, 1)
Kosta Barbarouses (Melbourne Victory FC, Australia, 44, 4)
Myer Bevan (Vancouver Whitecaps FC, Canada, 2, 1)
Shane Smeltz (Borneo FC, Indonesia, 57, 24)
Chris Wood (Burnley FC, England, 53, 23)
Japan v All Whites International Friendly
When: Friday 6 October 7.20pm (11.20pm NZT)
Where: Toyota Stadium in Nagoya