Pupils from third class and up in primary schools are required to wear a face mask or covering, and any claim that a child is exempt must be backed up by a medical certificate, the Department of Education has told schools.
In guidance sent to schools, it says that where a medical certificate is not provided a child or staff member will be refused entry to the school.
However, it also states that in some cases schools will be best placed to identify children whose complex needs are such that the wearing of face coverings may not be possible for them and in such circumstances a medical certificate will not be required for exemption.
The direction is far stronger than was expected, and has been met with shock by some school principals. One school principal, speaking to RTÉ News, said the instruction at short notice was disrespectful to children and school communities.
Earlier, schools had issued notices to parents stressing that the wearing of masks was a recommendation from NPHET and was not mandatory.
The Department of Education told RTÉ News that while the instruction regarding face masks applies from tomorrow, schools should show "flexibility" for the first couple of days, while families become accustomed to the new procedures.
Children from third class and up must also wear face coverings if they take a bus to school under the primary transport scheme.
The department said a medical certificate must be supplied to show that a child has difficulty breathing or another relevant medical condition, is unable to remove the cloth face-covering without assistance, or has special needs and may feel upset or very uncomfortable wearing the covering, for example pupils with intellectual or developmental disabilities, mental health conditions, sensory concerns or tactile sensitivity.
It says that in the limited circumstances where a face mask or covering cannot be worn, clear visors must be considered.
The department says that where children from different classes are mixed in a single classroom, only children in third class and above are required to wear face masks.
It says parents should be advised to get face masks for their children which fit properly and are comfortable, but that schools "should have a sufficient supply" to replace masks when needed.
The guidance states that face masks/coverings must not contain any slogans/logos/images that may cause upset or be deemed offensive to any member of the school community.
It says information should be provided by schools on the proper use, removal, and washing of face coverings, and that masks should be stored in a designated space, for example, in an individually labelled container or bag.
However, one school principal has told RTÉ News that he and other principals he has been in touch with this evening are shocked at the short notice and the lack of detail in the communication.
Enda McGorman of Mary Mother of Hope School in Dublin 15 has complained that there is no effective date of implementation mentioned. He says that schools do not know whether children can take their masks off in the yard, or take any mask breaks during the day.
"We want to persuade people that mask wearing is in everyone's best interests, but saying that it is 'required' is very forceful and very strong", he said.
He said the instruction was "ill thought out" and was leaving schools in a very difficult position.
"Sending out an instruction like this, with no lead-in time, is disrespectful to children and their parents and school communities.
"We are very anxious that schools are safe for children but we need a lead-in time."
However, Mr McGorman said he believed that school leaders would use their own judgement and be conciliatory in the implementation of mask wearing.
'Mask wearing not a silver bullet' - Donnelly
Meanwhile, the Minister for Health has said that mask wearing is not a silver bullet nor are any other measures and schools require numerous layers of protection.
"The mask is just one measure of many," Stephen Donnelly said.
He also defended the government's decision to stop contact tracing in September and said the decision was taken to focus on where transmission was occurring most instead.
Speaking on RTÉ's Prime Time he said that there are very different views among experts on CO2 monitors and a sub group within NPHET and others are providing the recommendations to the Government.
He also warned that there is a need to be careful about jumping to conclusions with high cases among school children and believing it is happening in school settings.
He added that the advice he is getting is that the majority is occurring outside schools.