Edinburgh City Council, Fife Council and Dumfries and Galloway Council all said remote learning may have to be considered as the pandemic continues to rip through teachers and pupils.
Director of education for Dumfries and Galloway council, Gillian Brydson, said individual classes or year groups could face the return to online learning despite the easing of restrictions.
This is due to rising case numbers, she said, leading to “very challenging” situations for “a number of our schools and early years settings”.
The return of remote learning, brought in during the early stages of the pandemic, could come “as a direct result of staff unavailability”, Ms Brydson told parents in a letter.
Pupils are just weeks away from sitting their exams, some of whom will never have sat formal exams in their school career.
She said: “Please be assured that we would only ask pupils to do this if the situation is unavoidable, because of health and safety concerns due to staff absences, and for as short as possible," she said.
"Your headteacher will try and communicate with you as soon as possible if this change to remote learning needs to be implemented and affects your child.
"The next few weeks are very important ones in our school year, particularly with exams and school transitions.
"I am working with our headteachers to ensure that we prioritise these important aspects of our young people's learning."
The council official added that there was “some light at the end of the tunnel” in regards to Covid as restrictions begin to ease.
Shelagh McLean, head of service at Fife Council, said it too was facing a “high number” of staff absences and that it was “managing” them to keep schools open.
However, she warned that if staffing situations become “critical”, the council will “minimise” the impact of blended learning on pupils.
She added: “So far none of our schools have returned to blended learning for the whole school.
"However, over the next two weeks where a staffing situation in a school or an area is critical, we will work to minimise the numbers impacted by any move to blended learning as we have done throughout the pandemic."
A spokesperson for Edinburgh City Council confirmed they were also considering a return to remote learning should existing mitigations be “exhausted”.
These include “deploying central staff” and sharing staff across schools.
A spokesperson said: “Our staff are working under immense pressure to continuing to provide teaching and learning however we are experiencing high numbers of staff and pupil absences at the moment.
"Keeping children at school remains our priority but ultimately if these measures are all exhausted remote learning may be considered.”
A Glasgow City Council spokesperson said “many” schools in the city were affected by both staff and pupil absences.
They said: “In-person learning remains our priority. Staff and young people are reminded to continue to follow the advice and guidance to help suppress the spread of the virus along with the mitigations already in schools to help achieve this.”