Existing mitigation measures, such as masks in high schools, social distancing requirements and enhanced cleaning and ventilation in schools, will be in place for six weeks and then reviewed.
EIS general secretary Larry Flanagan said he had sent a bulletin to members last week, highlighting the need for the continuing application of safety mitigations in all schools.
He said: “Most school staff will now have received their vaccinations, which offers a degree of reassurance, yet the majority of young people will not have received any form of vaccine.
"The continuing emergence of new strains of the virus, against which the vaccines may offer less protection, increases the risk of further outbreaks within our school communities. It remains essential therefore that schools continue to exercise all due caution in rigorously applying continuing safety mitigations to reduce the risk of Covid outbreaks.”
Mr Flanagan continued, “Following an agreement with the Scottish Government and local authorities, schools have re-opened with largely the same mitigations that were in place pre-summer.
"This is a sensible step that will reduce the risk of sudden Covid spikes linked to school communities.
"Physical distancing and use of face coverings are continuing on largely the same basis as before the summer, while other measures such as enhanced cleaning and the provision of adequate ventilation in all classrooms remain vital to making our schools as safe as possible for pupils and staff.
"Case numbers over the summer period continued to be a cause for concern, particularly amongst younger people where many will not have been vaccinated against Covid.”
Mr Flanagan added: “The roll-out of the vaccine programme has allowed the country to move out of lockdown and lift many restrictions, but it is very clear that the virus has not gone away and remains a threat – particularly to those in vulnerable groups.
"The EIS continues to expect local authorities to take all possible steps to protect pupils and staff within those groups, including the continued ability to work from home for those who are clinically extremely vulnerable.”