A family bereavement has resulted in the Barrett brothers, Beauden, Scott and Jordie, not leaving with the team from Auckland on Saturday morning. They should rejoin the All Blacks in Tokyo midway through next week.
Lock Sam Whitelock and Will Jordan have inner ear issues and have stayed home and will join the tour when they are both cleared to travel.
Coach Ian Foster said Whitelock was progressing well with the issue and was a possible starter when the team reaches Britain for their Test against Wales. Jordan was less certain.
Also unable to tour is halfback Folau Fakatava, who ruptured the graft to his ACL while doing his own training on Thursday.
Foster said it was sad for Fakatava. He added that the injury needed further assessment to determine if it would recover naturally or require more surgery.
"It's devastating. He's worked hard, he was excited about the tour and this next game [against Japan] was a big opportunity for him," he said.
Hooker Dane Coles has a niggle which is progressing well, but they have called in Asafo Aumua as cover for him.
Other players who got the unexpected call to join the side were lock Patrick Tuipulotu for Whitelock and halfback Brad Weber. Weber will be with the side for the Japan game. A reassessment will be made after that game with a possibility that TJ Perenara may join them afterwards.
He wasn't considered for Japan, as he is playing the Bunnings NPC final on Saturday.
Also joining them is Damian McKenzie as cover for Beauden and Jordie Barrett.
The players called up were all named in the All Blacks XV to play Ireland A, and the Barbarians. They are expected to join them when the Barretts and Whitelock return to the side.
Foster said it wasn't a setback for the tour plans - it was more of a readjustment.
Japan would be well-primed for the All Blacks after three games against Australia A, and the match was much more of a contest than earlier stop-offs at the start of northern tours.
"They've got some big scalps under them, they've got a proven programme and some of the noise out of there is they are extremely confident about the game. It changes the mindset, so for us it is a tour of four Test matches."
Six squad members will remain in New Zealand with an aim to join the tour at a later date.
Beauden, Jordie and Scott Barrett (family bereavement, will arrive in Japan mid-week).
Folau Fakatava (knee - ruptured ACL graft).
Samuel Whitelock (inner ear).
Will Jordan (inner ear).
Four players have been brought in as cover from the All Blacks XV:
Asafo Aumua (cover for Dane Coles who is managing a mild calf issue).