The Manchester United midfielder has yet to join up with the rest of the Scotland squad after being struck down with tonsilitis. However, Scotland manager Craig Levein is hopeful Fletcher will be available for their final Group I match against world champions Spain in Alicante on Tuesday.
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 returned to Scotland duty last month following a long absence caused by a mystery virus and made his first international appearance this year in the 2-2 draw against the Czech Republic.
Scotland are third in their group, trailing the Czechs by two points in the race to secure second place. Levein's side need to win their last two matches and hope the Czechs slip up against Spain on Friday and then Lithuania next week to snatch a play-off spot.