Head teachers around the country have now been ordered to ensure that youngsters and parents are made aware of the rules which are enforceable by law.
Groups of parents at school gates are also emerging as potential means of spreading the virus, National clinical director Professor Jason Leitch warned during today's daily Coronavirus briefing.
Anyone returning to Scotland from a foreign country, which does not have an "air bridge" with Scotland, must self-isolate for 14 days.
But Prof Leitch told today's briefing: "The Scottish Government has been informed by our directors of public health about a number of cases of children and young people being in school after recently returning from countries not exempt from quarantine rules.
"The law requires that everyone returning to Scotland from non-exempt countries to self-isolate at home for 14 days.
"This includes children as well as adults. People self-isolating should not go out to work, school or visit public areas."
France, Spain and Portugal are among the countries which are not exempt and would require people isolate.
"Scotland's directors of education will be speaking to head teachers and heads at early learning and childcare settings today to ensure this is made clear to parents, children and young people," Prof Leitch added.
Recent activity from the Scottish Government's "Test and Protect" regime to stem the spead of the virus has also flagged up concerns about people meeting up outside schools.
"This includes parents gathering at school gates, young people meeting friends without following the guidance on physical distancing," he added.
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