The Manchester United midfielder has yet to join up with the rest of the squad after being struck down with tonsilitis.
However, Scotland manager Craig Levein is hopeful he will be available for their final Group I game against Spain in Alicante on Tuesday night.
A statement from the SFA confirmed: "Darren Fletcher will not travel to Liechtenstein due to tonsillitis but remains in contention for Spain and his progress will continue to be assessed by medical staff."
Fletcher, who played 90 minutes as Manchester United beat Norwich 2-0 on Saturday, had recently returned to the international fold following an absence through illness.
Earlier today, Wigan midfielder James McArthur was called into the squad after Robert Snodgrass pulled out with an ankle injury.
Blackpool pair Stephen Crainey and Matt Gilks were also forced to withdraw and were replaced by Lee Wallace and Cammy Bell.
The Scots are still sweating over the fitness of striker Kenny Miller, while Alan Hutton is also nursing an injury.
Miller has a minor tear in his groin and is likely to miss Saturday's clash against Liechtenstein in Vaduz, but the Cardiff striker is hopeful of being fit to face Spain.
Hutton sat out training yesterday with a knee problem.