With schools set to return on Monday after a two-week break, unions and principals have raised concerns over social distancing and staffing numbers.
Education Minister Peter Weir insisted yesterday that schools remained "a controlled environment" despite one in every 20 pupils being absent because of self-isolation or shielding in the week before half-term.
Speaking to the BBC, Mr Weir said that while all risk could not be avoided, it was vital that children returned to schools.
He also called on parents to do everything possible to make sure community transfer of the virus was kept to a minimum.
But Justin McCamphill from the NASUWT, Northern Ireland's largest teaching union, said enforcement of guidelines was not strong enough.
"In our view, there are no extra mitigations. Children are already required to wear face coverings on public transport but, unfortunately, this is not being enforced in any meaningful way," he told the Belfast Telegraph.
"If the problem was simply parents congregating at school gates, that could be fixed very easily. The reality is that transmission is occurring within schools. Therefore, the minister needs to be implementing mitigation measures in schools.
"He needs to be looking at face coverings for children in classes and he needs to look at how two-metre social distancing can be put in place."
Mr McCamphill also called on Mr Weir to make use of the Education Training Inspectorate to make sure schools followed the guidance.
Liam McGuckin, the vice-president of the National Association of Head Teachers and the principal of Greenisland Primary School, said his main concern was finding substitute teachers if staff had to self-isolate, having struggled to cover one of his classrooms before half-term.
"I rang 15 people on the sub list and everyone was in fairly long-term employment," Mr McGuckin explained.
"My worry would be if we got into a situation in two or three weeks where we had to contact parents and say, 'Sorry, we have no one to teach the class'."
He said the current regime of keeping pupils in classroom bubbles had worked well and that most parents were observing social distancing when dropping children to school. "Educationally, we're getting through a lot of work. The children are very settled and happy," he added.
"The worry would be that if figures do stay high and teachers become infected, we don't have access to the substitute teachers that Mr Weir believes are there."
Stranmillis Primary School principal Jackie Wallace said it was crucially important for schools and parents not to drop their guard.
"I think we're all concerned at the rising numbers. I think society in general has got to be careful about social distancing and about hand washing," he added.
"From our perspective, that includes parents leaving their children off at school. It's important to keep distanced at the school gate."
From Monday, new measures at the school will include asking teachers to wear face coverings in corridors and while in the staff room.
Staff will also have to make sure rooms are well ventilated to "cut down on the possibility of airborne transmission".