Experienced playmaker Mo'unga suffered a torn calf muscle during a midweek training session, meaning he'll miss Saturday's first Bledisloe Cup Test in Auckland and the second match in Sydney a week later.
It is unclear if the 32-year-old will also be unavailable for the All Blacks' four Nations Championship Tests in the United Kingdom in November.
Coach Dave Rennie was already without Ruben Love, who started six of the team's seven Tests this year at fly-half.
Love is to undergo ankle surgery, ruling him out for the remainder of the year.
Rennie may hand the number 10 jersey to 145-cap veteran Beauden Barrett, although the 35-year-old hasn't been favoured this year, used only once as a replacement.
The All Blacks will also be without Fehi Fineanganofo for the Bledisloe Cup Tests after the winger failed a concussion test.
Rennie is missing several injured squad members involved in the recent 3-1 series loss to world champions South Africa, including captain Ardie Savea.
Others unavailable include forwards Luke Jacobson and Patrick Tuipulotu, and backs Caleb Clarke, Anton Lienert-Brown and Billy Proctor.
The New Zealand and Australia starting teams will be named later on Thursday.