The five eighths' return to action after a seven month sabbatical ended in a collision during the Super 15 final and scans have revealed some damage to his right leg.
It's understood the Crusaders will release details later today about Carter's injury and rehab programme but he will not be available for the start of the Rugby Championship.
Indications were that he had suffered some structural damage.
Carter played his 100th test against England at Twickenham last year before going off with injury and into his reconditioning.
He returned to Super rugby after the June break and played at second five eighths outside Colin Slade as the Crusaders advanced to the final against the Waratahs.
Carter damaged his leg when he ran into a midfield tackle and he left the field soon after when he attempted a clearing kick and could not sustain any weight on his injured leg.
His injury means Aaron Cruden will be favoured to continue at first five eighths when the All Blacks meet the Wallabies in Sydney on August 16 as they attempt to achieve a world record winning sequence of 18 victories.
