Secondary pupils will still be expected to wear face coverings in classrooms as they return to school after the October break.
The students, as well as staff in both primary and secondary schools across Scotland, will also have to wear a mask in communal areas and when moving around the building.
On Tuesday, the Scottish Government said it had made the decision to keep the existing Covid-19 safety mitigations in place following advice from senior clinicians.
The chief medical officer, Dr Gregor Smith, advised that a more cautious approach would allow more time for 12 to 15-year-olds to take up the vaccination.
Education secretary Shirley-Anne Somerville said: “In recent weeks we have seen the previous sharp decline in Covid-19 case numbers starting to level off, and that is why we have decided to adopt a cautious approach and maintain safety mitigations in school for the time being.
“Progress with vaccinating 12-15-year-olds has been remarkable and is already over 40%.
“However, this was only rolled out a few weeks ago and allowing further time will mean that that encouraging figure rises even higher.
“This decision is based on advice from senior clinicians and takes account of the most recent data. We will continue to monitor case rates on a weekly basis, with a view to lifting restrictions at earliest possible time.
“While I fully understand that this will be disappointing news for some young people and their parents, as has been the situation throughout, the safety of children, young people, and all education staff remains the overriding priority.
“There is no room for complacency and we must all continue to remain vigilant to reduce the spread of Covid-19.”
Teachers’ leaders welcomed the move.
Larry Flanagan, general secretary of the EIS, said the union had “argued for great caution in any easing of school mitigations, especially in light of continuing high levels of infection and the incomplete rollout of vaccinations for pupils”.
Mr Flanagan added: “The priority is to keep schools open but as safe as possible, so this delay from the Scottish Government, with regard to easing mitigations, is welcome and will allow, also, more time for ventilation challenges to be met ahead of winter.”
MSP Oliver Mundell, the Scottish Conservatives’ shadow cabinet secretary for education, said the move will “come as a massive disappointment to pupils and parents given the SNP strongly indicated that masks in classrooms would end after the October break”.
He added: “Scotland’s schools should have been a priority for the SNP but with face masks in classrooms remaining, young people have once again been sent to the back of the queue.
“These glaring inconsistencies will be difficult to comprehend for pupils and parents, especially with such an incredible uptake of the vaccine in 12-15-year-olds.
“Pupils, parents and teachers need to see a plan from the SNP for a return to normal learning as soon as possible.”