The Scottish Football Association on Tuesday afternoon revealed the Scotland captain was not with the squad, who fly out to Switzerland on Thursday ahead of Saturday's clash in Vaduz.
A short statement on the SFA's website read: "Darren Fletcher is suffering from tonsillitis in Manchester but will be assessed by club and Scotland medical staff on daily basis."
Assistant manager Peter Houston revealed on Tuesday morning that there were two injury doubts on top of Kenny Miller's groin problem but did not mention the Manchester United midfielder.
Houston said on Tuesday: "We have got a couple of slight injuries that will not join us for training today [Tuesday] but will work with the physio and should be okay.
"Alan Hutton has got a wee bit of a knee injury and Robert Snodgrass has an ankle injury but nothing serious, and they should be able to join us."
Miller remains a significant doubt for the game against Liechtenstein on Saturday but he is confident of facing Spain.
The striker came off early in Cardiff's npower Championship clash with Hull on Saturday, but he is working with the Scotland physios and plans to travel with the squad.
Miller looks unlikely to be risked for the clash in Vaduz, with Brighton striker Craig Mackail-Smith set to step in, but the final group game in Alicante on Tuesday looks a realistic target.
Houston, speaking at the squad's base at Mar Hall in Renfrewshire, said: "Kenny Miller is still with us, he's progressing by the day.
"Kenny came up on Saturday evening and stayed here and the difference between Saturday and Sunday and him feeling better was quite amazing.
"It is going to be difficult perhaps for Saturday but certainly Kenny is more than hopeful and is still progressing. No-one knows their own body better than himself.
He is working away with the physios and hasn't joined our sessions yet.
"Saturday might be difficult but certainly for Tuesday I have high hopes for him."
Scotland only have three listed strikers in their squad, with David Goodwillie the back-up for Miller and Mackail-Smith, but the Cardiff striker's fitness doubt has not prompted another call-up.
"We haven't really spoken about bringing anyone else in with regards to that," Houston said.
"I think it will be as you are with regards to the striker department if Kenny doesn't make it."
Houston is confident Mackail-Smith can step in against Liechtenstein if required.
He said: "Craig Mackail-Smith is a bit similar to Kenny - he works very hard, is very, very quick and, more importantly he is scoring goals and in very, very good form."
Houston confirmed Kilmarnock goalkeeper Cammy Bell had replaced Matt Gilks in the squad.
The only other call-off was Gilks' Blackpool team-mate Stephen Crainey, who was replaced by Rangers left-back Lee Wallace on Sunday.