Schools will be allowed 'bank' hours for special education teachers to ensure students do not miss out.
In a statement issued to Newstalk, the Department of Education says it is conscious children may have missed an opportunity to get additional supports.
From January until the February mid-term break, schools will be allowed to bank hours.
It comes as some schools are forced to redeploy Special Needs teachers to deal with the shortage of substitute teachers.
A department spokesperson says while it has provided supports to schools, it also recognises that given the current high case numbers that "schools will continue to require additional substitute cover in the period leading up to the mid-term break (to 23rd February 2022) to assist in dealing with absences during this phase of the COVID-19 pandemic."
They say a range of measures have been put in place to increase availability of substitutes for schools - including flexibilities around student teacher availability.
And they say schools have been asked to make every effort to obtain a substitute for all teacher absences.
They add that non-classroom teachers, such as special education teachers and English-language teaching supports, should only be used "as a measure of last resort" where it was not possible to secure a substitute teacher through any other measures.
But they say: "Given the current level of employee absences across sectors, including the education sector, the department understands that some schools have on occasion had to use their non-mainstream, non-classroom teachers to maintain in-person education this week.
"The department is also conscious that there are numbers of children absent from school at present, either isolating as a result of COVID-19 or as a close contact.
"In these circumstances the department is conscious that these children may also have missed an opportunity to get additional support from their SET [Special Education Teaching] and is now permitting the banking of SET hours from January until the February mid-term break, in line with all of the additional measures to support schools during this phase of the pandemic."