Celtic's David Turnbull, Livingston's Robby McCrorie and his brother Ross of Aberdeen have tested positive for Covid-19 after being away on Scotland Under-21 duty.
In total 11 squad members and two staff are self-isolating after the players returned to their clubs following Tuesday's defeat in Greece.
Scot Gemmill's squad flew back to Scotland on Wednesday, and the trio must isolate for 10 days from 20 November, the 10 close contacts for two weeks.
It is the second time Ross McCrorie has tested positive after contracting the illness in March while on loan at Portsmouth.
"The close contacts were established using aircraft and bus manifests, in adherence to government protocols that consider close contacts to be two rows either side of a positive case," said the SFA in a statement.
Celtic then announced on Twitter that midfielder Turnbull returned a positive test, while Aberdeen have confirmed they will be without Ross McCrorie and close contacts Lewis Ferguson and Connor McLennan.
'Urgent answers required' over SFA 'shambles' - managers' reaction
Speaking on Sportsound, Parkhead manager Neil Lennon described the situation as a "shambles", adding: "Again one of our players goes away on international duty and picks something up, it's bitterly disappointing."
Motherwell have confirmed Allan Campbell and Barry Maguire will have to self-isolate despite both returning negative tests carried out by the Fir Park club upon their return.
"We were first notified of the potential need to exclude Allan and Barry at 9:30pm on Friday night," said a Motherwell statement."As a result of what has happened, we will write to the Scottish FA on a number of points on which we believe urgent answers are required."
The latest development comes after a member of the team's backroom staff returned a positive test last Sunday prior to the group travelling to Greece, with a colleague deemed as a close contact.
Aberdeen manager Derek McInnes is "extremely angry" to be deprived of three players for three games and questioned whether the Scottish FA fully adhered to Covid protocols.
"You'd like to think when your players go away the same protocols and regard to what we're doing is replicated. We don't feel that been the case," he told BBC Scotland.
"I'd like to think after a member of staff tested positive that everybody was tested again before they flew out of the country. My players sat where they were told to sit when they were away on coaches, on aeroplanes - this isn't my players sitting where they shouldn't sit or going to another room.
"There's no apology or remorse. There's certainly things that can be done better. We would like more guarantees and assurances."
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