Education Minister Norma Foley has acknowledged the return to schools on Thursday 'will not be without challenge'.
The Department of Education confirmed on Tuesday that schools will re-open as planned.
Following a meeting between Minister Foley, unions and stakeholders the department said there was "no public health rationale to delay the re-opening of schools later this week".
But Minister Foley told Newstalk Breakfast it will not be easy.
"I will acknowledge it will not be without challenge, I absolutely accept that.
"Every sector of society is challenged in terms of personnel being in place.
"But the most important factor here is that we are opening, and schools will operate to their maximum capacity as and from Thursday."
Asked specifically about staffing shortages, she says there will be a priority list for classes.
"I think the reality is there are going to be ongoing challenges for a number of weeks here.
"There is a very clear hierarchy of priority in terms of students - in terms of particular provision being made for special schools and special classes.
"Younger children who cannot engage in the remote teaching and learning, and obviously at second level for exam students".
The general-secretary of the ASTI, Kieran Christie, earlier said some of his members have 'grave unease' around returning to classrooms.
He also said it "beggars belief" that they have been arguing for the use of medical grade masks in schools for 20 months.
"People are still going in with all manner of cloth face coverings and so on," he said.
Asked about the use of medical grade masks, Minister Foley says this is being reviewed in line with public health advice.
"That is an issue that has been raised by the teaching unions, and there has been a commitment by public health to review that very specifically.
"And if it is their recommendation, if there needs to be a change there, we absolutely will implement it".