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Israel Dagg, who would have deputised for Muliaina at fullback is also out of the Japan clash on Friday as the All Blacks elected not to risk their stars before their crunch game against France the following week.
McCaw, Muliaina and Dagg were all injured during a training session late on Wednesday and the players failed assessments by the All Blacks medical staff on Thursday morning.
"It’s disappointing to have the players unavailable, especially Richie and Mils who were both looking forward to playing against Japan," coach Graham Henry said.
"But injuries are something that we all have to deal with and it’s great that we have versatility in the squad so Isaia (Toeava) is able to slot in at fullback."
Carter was pulled from the side just hours after the team to play Japan was named on Wednesday as he continues to be troubled by a sore back suffered in the All Blacks opening match against Tonga.
McCaw, who was due to play his 100th Test, has suffered a minor calf strain in his left leg, and Muliaina has a tight right hamstring, team doctor Deb Robinson said.
Dagg, who would have covered for Muliaina has a right abdominal strain.
"It was a bad day at the office as far as injuries are concerned but the good news is that all the injuries are not serious," Robinson said.
"There would be risk of further injury to these players if we let them play so we have withdrawn them.
"We will now concentrate on their rehabilitation with the aim of getting them ready to resume training next week to prepare for the France Test."
Japan coach John Kirwan said the absence of McCaw and Muliaina would have no effect on his side but it could disrupt the cohesion of the All Blacks.
"I'm disappointed for them, obviously they've picked up a few niggles, but it doesn't change anything for us," he said.
"Things like that are probably a coach's worst nightmare. It creates disruption and certainly doesn't help your build up, but the All BHlacks have been together enough and played together enough I don't think it will affect them too much."
Hooker Keven Mealamu will now captain the side with Toeava, who was not named in the original match 22, starting at full-back.
The forwards reshuffle sees Adam Thomson move to openside flank, Victor Vito comes off the bench to number eight and lock Anthony Boric replaces Vito in the reserves.
The All Blacks ranks were hit by injuries even before the tournament started with first-choice number eight Kieran Read suffering an ankle strain last month and unlikely to play before their last pool match against Canada on October 2.
Thomson, who suffered an elbow injury in the same Test against Australia that sidelined Read, only returned to full training this week.
With loose forwards bearing the brunt of the injuries and McCaw's unavailability again reducing their stocks to the bare minimum of three, lock Sam Whitelock is the designated replacement.
While Carter is unavailable, scrum-half Piri Weepu will be on the bench as the back-up flyhalf, a position he has regularly played in during the Super rugby competition.
