Arsenal and Celtic questioned self-isolation rules for their players after Stuart Armstrong's positive test for coronavirus ruled him and teammates Kieran Tierney and Ryan Christie out of Scotland's crucial Euro 2020 play-off semi-final against Israel on Thursday.
The Scottish Football Association (SFA) said on advice from the Lothian Health Protection Team, Arsenal defender Tierney and Celtic midfielder Christie would be forced to self-isolate for 14 days after being in close contact with Southampton's Armstrong, who would be quarantined for 10 days.
All three will also miss Scotland's Nations League clashes with Slovakia and the Czech Republic.
On top of that Tierney would be absent for Arsenal's trip to Manchester City in the Premier League on October 17, while Christie would miss the first Old Firm game for 10 months against Rangers the same day in the Scottish Premiership.
"Our medical team have confirmed that Kieran was socially distant at all times from the player who tested positive and has broken no rules regarding COVID-19 protocols," Arsenal said in a statement. "We are currently seeking further advice and clarification of the details.
Celtic also issued a statement saying: "Celtic confirmed today that it aims to open dialogue with the Scottish Government and other authorities to fully understand the self-isolation procedures for those players who continue to deliver negative test results, as Ryan has."
Tierney and Christie also expressed their frustration at the measures.
"I'm so disappointed and frustrated to be in this situation. I have adhered to all regulations and made sure I was socially distancing from my team mates in the hotel. I've also tested negative," said Tierney.
In Celtic's statement, Christie added: "I am so disappointed by the events of today and the potential effects this could have on my country and club
"As I have operated within these protocols for such a long time now, I am well aware of all the rules and social distancing from team mates has become the norm and something I have observed.
"The situation is very frustrating, particularly as I don't believe I have done anything wrong."
Arsenal boss Mikel Arteta had voiced his fears over releasing players on international duty and more battles between clubs and national associations are expected for November's international break.
Scotland manager Steve Clarke admitted his plans had been thrown into disarray with three key players ruled out the day before one of Scotland's biggest matches in years.
Clarke's men are two games away from a first major international tournament for 22 years. Beat Israel on Thursday and they will face Norway or Serbia in November for a place at next year's postponed Euros.
"We were working towards one team and now we have to change that," added Clarke.
"We moved the training back to this afternoon. We have a little bit of time to work on one or two different things, one or two different players coming into the team that maybe didn't expect to play.
"Although it is disappointing for the ones who have had to drop out because of the situation, the ones who are going to get a chance to play - what an opportunity."
Stricter coronavirus regulations will be introduced in Scotland from Friday to curb a rising number of infections, but professional sport will continue to have an exemption to keep playing.
"It is something that is there, it is in everyone's lives now, we have to adapt as much as we can and be prepared for," said Clarke. "I tell the players that they have to be ready to step in at any time because we need everybody."