The 25-year-old, who replaced injured first-choice Finn Russell in the defeat against Ireland in the Six Nations earlier this year, was expected to join up with the Scotland squad once more.
However, Scotland boss Vern Cotter, who will be replaced by Glasgow head coach Gregor Townsend in June 2017, will have to find an alternative to the Edinburgh man.
Harlequins’ Ruaridh Jackson was chosen as lead stand-off for the Test series in Japan with Russell injured, and is expect to be chosen as Russell’s back-up after the Glasgow stand-off returned from injury against Ulster last weekend.
Meanwhile, Edinburgh will have to wait to determine the extent of the damage suffered by Kevin Bryce after the tighthead injured his elbow in the match against Munster. He will likely miss Edinburgh’s clash with Connacht on Friday.
Loosehead prop Alasdair Dickinson continues to recover from a hamstring injury sustained in Scotland’s summer tour to Japan and is expected to return to training late in October.