Secondary pupils will continue wearing masks in class for the first six weeks of the new term - but close contacts of those with Covid will no longer be required to self-isolate, provided they have a negative PCR test result.
First Minister Nicola Sturgeon announced the change during a statement to MSPs on Tuesday afternoon.
It follows a decline in the coronavirus case rate and comes as schools prepare to reopen after the summer holidays.
Ms Sturgeon said: “If a young person aged 5 to 17 is identified as a close contact, they will need to take a PCR test – but they can end their self-isolation if they test negative.
"Children under the age of 5 will be encouraged but not required to take a PCR test.
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"This means that the blanket isolation of whole classes will no longer be routine. Instead a more targeted approach will identify close contacts at highest risk of infection.
"So fewer young people will have to self-isolate, and most will be asked to self-isolate for a much shorter period of time."
She added: "For up to six weeks - subject then to review - there will be a continued requirement for staff to keep at least 1 metre distance from each other and from children and young people while on the school estate.
"We have also decided, after careful consideration, to retain the current requirements for face coverings in schools for staff and for children aged 12 or over. That includes asking young people and staff in secondary schools to wear face coverings during lessons, and while inside school buildings."
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As part of plans to boost ventilation, all schools and day care services for children have also been told they must have access to CO2 monitoring through either fixed or mobile devices. These are to be used to assess quality and identify necessary improvements. Stressing that she expected this process to be completed by the October half-term, Ms Sturgeon added: "I can... confirm today that we are making available to local authorities an additional £10 million to support this work."
In addition, councils and schools will ask all secondary pupils and staff to take a lateral flow test one or two days before they return after the holidays, and then twice a week after that.
The First Minister also said work with the further and higher education sectors on plans for the coming academic session was ongoing.
The changes announced - particularly those affecting self-isolation arrangements - could have significant implications for the decision on whether to hold a normal exams diet next year.
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Last term, all pupils identified as close contacts of a positive case were forced to isolate for ten days - even if subsequent tests came back negative. This brought major disruption to youngsters, their families and schools.
Ms Sturgeon's announcement was broadly welcomed by the EIS teaching union.
Assistant Secretary David Belsey said: “We agree the continued wearing of facemasks, physical distancing measures, effective ventilation of classrooms and good hygiene regimes need to remain in full force.
"The Scottish Government’s acknowledgement of the importance of strengthening the guidance around ventilation and the additional funding to close any gaps in this provision is extremely welcome and a significant improvement to the current mitigations.
“The completion of vaccination programmes for all school staff is vital and the EIS believes that voluntary vaccination of 12 – 17 year-olds would be sensible and may go some way towards making schools safer places and help to address the anxieties of some young people.
“The six week period of no changes to mitigations will provide a degree of reassurance to school staff and some certainty as to what to expect when returning to classrooms.
"This will also allow for meaningful consultation between Scottish Government, Local Authorities and teachers’ unions before any further changes. The EIS will study the new guidance and seek to address any emerging issues with the Scottish Government and employers.”
Jo Bisset, organiser for UFTScotland, said: “While nightclubs reopen and football fans flock in their thousands to stadiums across the country, kids will still have to stew in masks all day.
“This means children will be forced to wear coverings for considerably longer than almost any adult doing any job – that’s unacceptable."
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