The 29-year-old will self-isolate and not travel for Wednesday’s friendly against the Netherlands in Portugal.
The Scottish FA says the rest of the squad recorded negative results on Tuesday after being retested.
Steve Clarke’s side have a further friendly, against Luxembourg on Sunday, before their Euro 2020 opener against Czech Republic at Hampden on 14 June
Sheffield United’s Fleck was part of the 26-man squad named by Clarke for the delayed finals, Scotland’s first major tournament in 23 years.
Clarke and his players flew to Spain four days ago to prepare for the Euros at the LA Finca resort.
Scotland were deprived of key trio Stuart Armstrong, Kieran Tierney and Ryan Christie for the play-off semi-final win over Israel in October after the former tested positive and the two others had to self-isolate as close contacts.