Stuart Hogg has had an operation on a damaged bone in his wrist and, according to his club coach at Glasgow, Gregor Townsend, is unlikely to be available for next month's internationals against Japan, South Africa and Australia,
Hogg should return soon after that but the news is worse for his Warriors team-mate Peter Murchie, who is likely to miss the entire Six Nations.
Murchie, who took Hogg's spot during Scotland's summer tour to South Africa, while the latter was on British & Irish Lions duty, dislocated his shoulder playing for Stirling County last month. He has also had an operation but the recovery time is much longer.
Both injuries disrupt plans just as Johnson is starting to pencil in names for the extended squad he will invite to a training camp two weeks ahead of the opening match. Also unlikely to be involved is Tommy Allan, the dual-qualified fly-half who represented Scotland through the age groups but has now been invited to train with Italy, his mother's homeland and the country of his birth.
"I have spoken to Tommy. What I said will remain private but it is really simple from my point of view: I only want people who want to play for Scotland in my team," Johnson said at the Glasgow launch of a charity single recorded by the Scotland squad, featuring the Frankie Miller song Bottle of Whisky.
"It is really simple and I won't go back on that. The players are the custodians of the jersey just as I am the custodian of the coach's spot, and the fact is we only want kids out there who want to play for Scotland."
Nevertheless, it seems the teams for the November matches are likely to have an experimental look. "I am going to have to do a bit more searching," Johnson said. "The new head coach starts in the middle of the year and I want to make sure there is a good understanding of where players lie. It is important that we do that now; I don't want to be chasing my tail in 2015."