The 32-year-old Carter was using provincial rugby to work back into match fitness ahead of the All Blacks' third Bledisloe Cup clash with Australia on October 18 after breaking his leg in the Super Rugby final.
He played 40 minutes against Southland last week but was bothered with a calf injury and failed to convince Canterbury coach Scott Robertson he would be able to get through the game in Christchurch.
"He bruised his calf in last Sunday's match against Southland and although he has been recovering well, was ruled out of contention at today's captain's run," the team said.
Carter has barely played at all this year after he was given a six month sabbatical by the New Zealand Rugby Union with a view to having surgery on niggling injuries and work on his conditioning in order to ensure he was in peak physical form at next year's rugby World Cup in England.
He returned to first class rugby off the bench for the Canterbury Crusaders in the final few rounds of Super Rugby and was playing well before he broke his leg against the New South Wales Waratahs during the final in early August.
He had originally expected to be out for about a month, then said he hoped to be considered for the All Blacks' final two Rugby Championship matches against Argentina and South Africa.
He missed both deadlines and was released by the All Blacks' squad to work on his match fitness with an eye to being available for the third Bledisloe game against the Wallabies before their end-of-year tour to the United States and Britain.
Canterbury's final regular season game is on October 12 away to Taranaki but it is unclear whether All Blacks' coach Steve Hansen would be willing to allow Carter to play the game if he still wants him to play in Brisbane.
The All Blacks, who have already clinched their third successive Rugby Championship title, face the Springboks in Johannesburg on Saturday.