McAlister is due to undergo knee surgery on Friday - the same day as his team-mates arrive in Cardiff ahead of their November 5 clash against Wales - and could be out for eight weeks.
Prop Greg Somerville could also miss the tour after tearing a calf muscle earlier this month.
Auckland forward Saimone Taumoepeau has joined the All Blacks training camp as cover, and a final decision on Somerville's fitness is likely to be made on Wednesday.
"It is disappointing news for Luke, and potentially for Greg as well," said All Blacks coach Graham Henry.
"The medical advice for Luke is clear - surgery is the best option. We are holding out a little hope for Greg, but he is in a race against the clock and we need to see significant
improvement in the near future."
And in a third setback for Henry, lock Ali Williams looks like missing the Wales encounter due to shoulder trouble.
Williams is currently sidelined from training, but initial medical assessments suggest he will be able to train next week, making him available for the November 12 appointment with Ireland in Dublin.