The changes comes into affect "as soon as possible" and means masks should be worn in all indoor spaces where social distancing is not possible.
This comes as new international travel rules are introduced and the booster vaccine programme is expanded to include all adults in Wales.
Education Minister Jeremy Miles said the change to mask rules was being introduced to ensure disruption was kept to a minimum during the final weeks of the school term.
He said: "We are now introducing an additional measure, while we learn more about this new strain.
"All staff and learners in our secondary schools, colleges and universities should now wearface coverings while indoors where physical distancing cannot be maintained.
"Many settings are already operating on this basis, guided by their local risk assessment, but this will now become a national approach.
"This is a temporary, precautionary measure that will be in place for the remaining weeks of term at which point the position will be reviewed.
"This should come into effect in all settings as soon as possible."
The Welsh Government also confirmed that all people aged 18 and over are to be offered a Covid-19 booster vaccine as part of efforts to tackle the spread of the new Omicron variant.
The Joint Committee on Vaccination and Immunisation (JCVI) is now advising that all adults aged 18 to 39 should be offered a booster dose, in order of descending age groups, to increase their level of protection. Those aged 40 and over are already eligible for a booster vaccine.
Booster doses should be given no sooner than three months after people have had their second dose of an original vaccine - shaving three months off the current six-month wait, according to the JCVI.
In further advice, young people aged 12 to 15 should be offered a second dose of the Pfizer/BioNTech Covid-19 vaccine, no sooner than 12 weeks after their first dose.
The JCVI also said that severely immunosuppressed people should be offered a booster dose no sooner than three months after completing their primary course of three doses.
Health Minister Eluned Morgan said: "The extent of protection COVID-19 vaccines will provide against the Omicron variant is not yet known, but the JCVI felt that accelerating the programme would maximise protection for individuals.
"Through extending eligibility and reducing the interval for booster, the aim is toreduce the impact of the new variant on the population, ahead of a wave of infection."
She also encouraged people to keep their vaccine appointments and that everyone eligible for a booster will "automatically receive an invitation to attend an appointment when it is their turn."