The New Zealand Rugby League (NZRL) released a statement on Thursday saying Hughes had been ruled out of contention after carrying a neck injury through the NRL finals.
Hughes' replacement, the NZRL said, would be "named soon".
The Melbourne halfback's absence leaves Stacey Jones short of an experienced playmaker, and it remains to be seen whether the new Kiwis coach can tempt retiring Warriors playmaker Shaun Johnson into a swan song.
The Kiwis, who face Australia in Christchurch on October 27 and Tonga in Auckland on November 2, are already without Dylan Brown, Kieran Foran and Te Maire Martin.
"Jahrome is understandably shattered and we really feel for him," Jones said in a statement.
"He has had an outstanding year and he was going to play a key role for the Kiwis again.
"He was desperate to play and we thought, with some time on our side, he would come right with treatment, but he has since received medical advice that he won't be ready to play."
As well as the absence of Hughes, Brown, Foran and Martin, Jones is without winger Ronaldo Mulitalo, hooker Brandon Smith and props Moses Leota and Nelson Asofa-Solomona.
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