It comes as a meeting between Minister for Education Norma Foley and representatives from teaching unions is due to take place on Tuesday.
General Secretary of the TUI Michael Gillespie said that, if teaching is to resume this week, schools will suffer serious staff shortages.
“It's not going to be one size fits all: we don't know how schools are going to be affected on Thursday,” he told Newstalk Breakfast.
“Over the next day or two... we're going to start finding out how schools are going to be affected; how many staff are not going to be there.
“We've now got texting and e-mail systems, so we'll be able to control who we can bring back on Thursday - if there is a need to reduce the number that are going to have to come back on Thursday because of the unavailability of teachers.
“Staffing is going to be a big issue on Thursday.”
Mr Gillespie said that the TUI is looking for clarity from the Government regarding Covid isolation periods, which will have a “big effect” on staff and pupils returning to school this week.
He said: “There's a lack of clarity now as to how many days they need to isolate: is it from their PCR, is it from their antigen test?
“That will have a big effect on the schools opening on Thursday - so we need that sort of certainty.
“We also need school guidelines to issue today about school autonomy, because we know that schools are going to be different.
“There's going to be difference in different areas where there's going to be staffing issues.
“We want to prioritise the exam years, obviously, special needs classes - make sure they're able to return if there are staffing issues in schools.
He added that issues around investment in ventilation are “not just about 2021 - that's about 2022, 2023 so that we have these comfortable classrooms that are well-ventilated.”
When asked if he believes schools will reopen as planned on Thursday, he said: “I hope so, but it's very hard to predict with the Omicron. We don't know how many people are affected yet.
“But I would certainly hope they would be opening as near to full capacity as possible, given whatever staff are available.”