Ania Kahl, from Edinburgh, says her 12-year-old son, David, was told to leave his English class at Broughton High School and sit in the corridor because he was not wearing a mask, even though he is exempt.
David, who has a medical problem with the veins in his nose and carries an NHS exemption card after having had two rounds of surgery to tackle the issue, was asked to leave the class with two other children, who both suffer from asthma and are also exempt from wearing a mask.
Ms Kahl said David had felt “very uncomfortable” after being told to leave the classroom and had phoned her at home.
"I told him to pick up his bag and come home,” Ms Kahl said. David, who is in S1, is only attending school one day a week at the moment and is required to work remotely the rest of the time due to Scottish Government lockdown rules.
All high school pupils should be returning to the classroom full time after the Easter holidays in two weeks.
Deputy First Minister John Swinney has said social distancing requirements will be dropped after Easter, although masks will still need to be worn by most pupils
Ms Kahl said: "He is only in school one day a week at the moment – that is the only time he can meet with other kids and get some education and he was just trapped outside.
"They are meant to be educating our kids. They are supposed to be in school to learn, not to sit outside of a classroom.”
She said the school had initially told parents there would be no exemptions in terms of mask wearing in the classroom when the Scottish Government first brought in the policy last year, but had backed down after an outcry from families.
Jo Bisset, organiser for campaign group UsForThem Scotland, said: “Children have suffered enough during the pandemic without having this new threat hanging over them.
“It’s completely unacceptable that young people with legitimate exemptions should be treated in this way. Of course all of this would be avoided if children were allowed to go about their school day without being forced to wear a mask.
“The Scottish Government’s own experts admit that the virus doesn’t spread among school children and that teachers aren’t at an increased risk compared to any other worker. The government has to act, otherwise more incidents like this will take place in coming weeks and months.”
A spokesman for Edinburgh City Council said: “All our schools are following the national guidance from the Scottish Government and health agencies in keeping our pupils and teaching staff safe. Our infection control mitigations are robustly enforced and pupils who have exemption cards do not have to wear face coverings.”