Children not wearing facemasks in school - who are not exempt from the measure - will be sent home, Education Minister Norma Foley says.
Students in 3rd class and above have to wear masks in school from Wednesday onwards.
New Department of Education guidelines state a medical certificate is required for an exemption, and those without evidence will be refused entry.
The Government is also calling for less indoor socialising among under-12s for the next two weeks, after a sharp increase in COVID-19 cases.
Minister Foley told Newstalk Breakfast the mask mandate is to protect all children.
"This is an expert public health recommendation, it is for the benefit of all children in our schools from 3rd class up.
"There has been extraordinary buy-in from students in our schools, and from parents and guardians, and from school communities as regards all of the public health measures that are required in our schools.
"And we have always, in the education sector, followed the recommendation of public health".
'Operated seamlessly at second level'
On masks specifically, she says this has already worked 'seamlessly' at second level.
"I recognise that there may well be issues of exception, where there may be difficultly for a child in terms of wearing a mask.
"A child with complex needs - for example - or if a child has any difficulty with breathing or other relevant medical conditions, there will be exemptions and they will be very clear exemptions in that respect.
"But I also want to say that this operates at second level, it has operated seamlessly at second level.
"And again there has been extraordinary buy-in from all concerned".
For those who don't wear masks without a medical exemption, she explains: "There has to be absolute clarity as to how the school operates.
"There is absolute clarity that there is a requirement and a recommendation from public health that for the benefit and protection of children, that those from 3rd class up would wear the masks.
"Students who do not comply, and do not have a medical basis, will be asked to stand down from school".
And she says this is part of other measures already in place.
"This is one measure in a suite of measures that operate within our schools.
"This is an additional measure - it is the expert medical view of public health and the NPHET here that it will be an additional protection for children.
"This is regarded as a protection for children - individually, collectively and the school community.
"We would wish that we were not in a COVID situation, we would wish that we are not in an emergency situation - and a challenging situation for our children and our communities - but we are".