The general-secretary of teaching union ASTI says some of his members have 'grave unease' around returning to classrooms.
Kieran Christie was speaking after the Department of Education confirmed that schools will re-open as planned on Thursday.
Following a meeting between Education Minister Norma Foley, teachers' unions and education stakeholders on Tuesday, the department said there was "no public health rationale to delay the re-opening of schools later this week".
It said the meeting was productive and all parties recognised the "the importance to students of in-school teaching and learning".
Ahead of the meeting, the ASTI had called for a staggered re-opening, with only exam-year students returning initially.
Mr Christie told Newstalk Breakfast they will follow the advice, but members are not happy.
"There remains enormous unease among our members regarding the health and safety of teachers and students in schools in the context of the Omicron variant.
"The truth is it hasn't been test-run, so to speak, in schools - it wasn't the dominant strain prior to Christmas, and people are understandably extremely worried around that."
He says they are calling for a staggered re-opening, as well as additional supports.
"It beggars belief that one of the additional supports that we're arguing for, 20 months into this pandemic, is that medical grade masks - which are quite cheap and available pretty much everywhere - be made the requirement in classrooms now.
"People are still going in with all manner of cloth face coverings and so on".
He says being in a classroom is akin to travelling on a bus.
"We have a position, longstanding, that we'll work with the public health advice.
"But that doesn't necessarily mean that our members don't have grave unease around the questions in relation to health and safety.
"People are very worried in the same way that people are worried about travelling in buses, even though they're being ran in a context of health advice and so on."
He also believes there is a "very strong possibility" that some classes may not be able to be taught due to staffing shortages.
"I'm getting varying accounts from principals around the country - anything from 10% to, at the higher end, 30, 40 and a worry that there might even be 50% in some schools of staff either [close] contacts or having COVID".
