Due to contact tracing or positive tests, 24,412 pupils and 2,200 school staff were isolating on Thursday last week, according to recent figures published by the broadcasting corporation.
A teacher, who preferred to remain anonymous, told BBC Scotland that it was "difficult" to maintain normal lessons with so many pupils off, as well as sending separate work to those who are isolating.
"As the term has gone on, particularly since the October holidays, we are looking at an increasing level of stress and anxiety," she said. "There is a feeling amongst teachers that what we are doing right now isn't really what we signed up to do.
"We are being called frontline workers but being given none of the protections other frontline workers have.
"They say everyone's safety and education would actually be in a better position if blended learning - that's some at home and some in school teaching - was brought in instead.
"I'm scared when I'm in work, but I'm also angry. It feels like we are going in there, we are doing this job and nobody is aware of the circumstances we are working in."
She said colleagues in schools across the country described the situation as "mayhem" and would prefer to move some classes online.
Another teacher said she was "scared and angry" while in work because of a lack of protection against the virus on top of mounting workloads.
A Scottish government spokeswoman told the BBC: "We appreciate this has been a difficult time for families and pupils and are grateful to all the teachers, school staff and many others who have worked hard to return some normality to young people's lives and keep them safe while they resume their classes.
"We are keeping the way guidance is being implemented in schools under close review, along with emerging scientific evidence, to help us to protect our school community.
"Where there is a need to take action, either by updating our guidance or ensuring it is being given practical effect, we will work with teachers, parents, trades unions, local authorities and young people's representatives to do so."