The second rower has sustained a calf injury, with head coach Scott Robertson opting not to call-up a replacement in the locks as of yet.
"All Blacks Captain Scott Barrett will miss the remainder of the Lipovitan-D July Series due to a calf injury sustained in the first test against France in Dunedin," a New Zealand Rugby Statement read.
"A scan on Monday has revealed a tear. Barrett's likely return to play is yet to be determined."
Speaking to the media from All Blacks training, assistant coach Scott Hansen confirmed that Ardie Savea will now take over the captaincy and provide further clarity on the injury.
"The process at the moment, medically, is that Scooter [Barrett] won't be available for the rest of the series, and there are just some options for us to consider and what that looks like in replacement of the group, so we're going through that at the moment," Hansen said.
"Yes [it's a calf injury], at this stage, it seems to be lower legs.
"So pretty much well on top of that, around what that process is through the medical but yes, a lower leg."
On a potential return to play date, he added: "We don't have one at this stage. I think we'll just take it week for week.
"He'll be keen to get back as quickly as possible, but we've obviously got to do what's right for him in the injury process."
A decision will be made on a replacement in the second row but Savea will skipper the team in the next two matches.
"Ardie will come in and lead us well, like he has for the last number of weeks," Hansen continued.
"We'll look at that [lock replacement], the boss, Razor, will go through that process and do what's best for the squad at the moment.
"Otherwise, training well today, everyone was up. We're obviously disappointed to lose the skipper, but we're going to go forward.
He added that the coaches are comfortable with the depth in the squad at the moment but there is bound to be a change in the team that beat France in the opening match.
"A replacement is something we will consider, obviously, there'll be a replacement there. We trust our depth, and there is an opportunity for someone else to step up," he added.
On the news of losing Barrett, he continued: "It's disappointing for us; he is a massive part of this team. What he has done well is grow the leadership group; we've got some outstanding experience there. It's a shared leadership model anyway.
"So, like anything, you adjust, and the leadership group will grab the team and go forward with it."