Carter kicked the matchwinning dropped goal in last weekend's 22-19 win over Ireland but tweaked his hamstring in training on Tuesday, allowing Aaron Cruden a chance to start the Test in Hamilton.
"Hamstrings are annoying things to anyone who's fast enough to have one. They tend to hang around for a bit," head coach Steve Hansen said.
"It should be a couple of weeks, three weeks, we're not really sure."
Cruden's inclusion is one of six changes to the starting XV which went close to surrendering the All Blacks' unbeaten record against Ireland.
Kieran Read's concussion has forced him out, with captain Richie McCaw moving to No 8 and Sam Cane taking his position at openside flanker.
Hansen also made four changes which he labelled "strategic", preferring not use what he called "that other word" - rest.
Luke Romano comes in at lock for Brodie Retallick, Liam Messam will play blindside flanker instead of Adam Thomson, and wings Hosea Gear and Ben Smith come in for Julian Savea and Zac Guildford.
"Right from the word go we felt that if this series was wrapped up by Christchurch, then we would look to make some strategic changes. We've done that with the four changes we've made," he said.
On the bench, hooker Keven Mealamu returning from injury as cover for Andrew Hore, Tamati Ellison will cover the outside backs, and Hurricanes fly-half Beauden Barrett could make his Test debut after being selected as cover for Cruden.
Hansen said he wasn't tempted to play inside centre Ma'a Nonu, who hasn't been on the bench during the Irish series, saying the All Blacks were using the three-week Irish series "to give him this opportunity to get a pre-season".
All Blacks team to play Ireland: Israel Dagg, Ben Smith, Conrad Smith, Sonny Bill Williams, Hosea Gear, Aaron Cruden, Aaron Smith, Richie McCaw, Sam Cane, Liam Messam, Sam Whitelock, Luke Romano, Owen Franks, Andrew Hore, Tony Woodcock. Res: Keven Mealamu, Ben Franks, Brodie Retallick, Adam Thomson, Piri Weepu, Beauden Barrett, Tamati Ellison.
