And former New Zealand Super Rugby player Crusader Johnny McNicholl is among the contenders to take his place.
He is one of three players likely to be considered by coach Wayne Pivac for the role. Hallam Amos, who has played eight times for Wales and Jonah Holmes are the others.
Williams' Scarlets club coach Dwayne Peel announced at a press conference on Wednesday that Williams had recently had his appendix removed.
Peel said Williams had an operation and was back with the club but was not expected to play before the All Blacks Test.
"It's just unfortunate timing for him and us really. He'll be out for this period. It's not clear yet but I can't imagine he'll play for us in this block of games," Peel said.
He said he may be available for later games for Wales during the November series.
Williams hasn't played since his last appearance on the Lions' tour of South Africa on August 7.
Pivac is already without frontline players first five-eighths Dan Biggar, wing Louis Rees-Zammit, No8 Taulupe Faletau and first five-eighths Callum Sheedy.
All four are employed by English clubs and, because the Wales-New Zealand Test is outside the November window, they are not required to be released.
Also missing from the Wales side will be another fullback, Leigh Halfpenny, who suffered knee ligament damage playing against Canada in mid-year, wing George North, loose forwards Justin Tipuric, Dan Lydiate and James Botham.
Former Blues and Otago utility back Michael Collins was considered a prospect for the Wales squad but suffered an injury in his most recent outing.