Secondary school pupils and staff will still be required to wear face coverings in communal areas after the Easter holidays.
They will also have to wear their mask when moving around the building.
It comes as the face covering rules for shops and on public transport are expected to be downgraded from legal requirement to guidance on April 4.
A Scottish Government spokesperson said: “Following the Easter break, face coverings will continue to be required in communal areas for staff and secondary school pupils.
“This is national guidance and these changes will be applied, and implemented, across all schools in Scotland.”
The spokesperson stated that the school-specific guidance on face masks and physical distancing will change on April 18.
They said: “Throughout the pandemic there has been school-specific guidance on face coverings and physical distancing. From April 18 that changes.
“Requirements regarding face coverings and physical distancing will be the same as those in place for other workplaces.”
Secondary school pupils have not had to wear masks in classrooms since February 28.
The face covering rules for shops and on public transport were also set to be eased on March 21 but were kept in place due to a spike in Covid cases.
According to the latest figures from the Office for National Statistics (ONS), one in 14 Scots are estimated to have had Covid in the week ending March 12.
And on Tuesday, 2221 people were in hospital with the deadly virus – which was the second day in a row a record high had been reached.
The surging number of cases have now begun to impact schools.
Local authorities across the country are reporting high rates of teacher absences, with some councils having to close schools or consider a switch back to remote learning.
Three nurseries, a primary school and a secondary school were either closed or partially-closed in the Highlands on Tuesday.
A spokesperson for Highland Council said: “Some schools are temporarily closed as staff members are following public health advice to self-isolate.
“Schools will update parents, carers, and pupils when they are ready to reopen.”