The ASTI says physical distancing is not being applied as it should be in some schools.
It comes as teachers belonging to the union are to be balloted for industrial action, amid concerns over health and safety.
ASTI deputy general-secretary Diarmuid DePaor told Newstalk Breakfast there seems to be double standards.
"The issues include issues about physical distancing and how it's happening in schools, about the provision of PPE, about what is a close contact and why is it different in a school than it seems to be anywhere else.
"There's a lot of concerns that the rules seem to be applied differently, in terms of if a case occurs in a school that what you do.
"If a case occurs in another workplace things get shut down, people get sent home and in school they don't - certainly not automatically.
"And there's a lot of confusion about that.
"We need faster testing: when there was a case in the Cabinet, the test result was there in a few hours - we have people waiting for days before they know what's to happen in a school because somebody is being tested.
"Provisions for high-risk teachers: we're still very concerned about teachers who may be high-risk on two or three different categories who may still end up being forced to be going into crowded classrooms, and we think that's putting unfair pressure in general on resources.
"We've had a lot of talks with the Government over the summer, we've been successful in some things but we're getting quite frustrated and people are getting quite fearful that the measures are not being applied as they should be and as strictly as they should be.
"I think it doesn't help that we've sought a meeting with the health people, and they've said 'no, talk through the Department of Health'.
"We have very, very genuine concerns, we are not health experts but we would like to meet the health experts face to face."
He said there are attempts at physical distancing "but in some schools it's practically not possible, and we are getting reports where it's not happening the way it should be.
"I mean it's already a narrower physical distancing than applies anywhere else".
A meeting of ASTI members at the weekend heard they have "serious concerns" about the health and safety of school communities.
ASTI President Ann Piggott said: "The fact that high risk teachers have been asked to work in crowded classroom is unacceptable to us as a trade union.
"The safety of students and their teachers must be the priority."
She said teachers are reporting that new work practices are being implemented without any consultation with school staff.
"It is unthinkable that at a time when teachers have demonstrated tremendous commitment to their students and to keeping education going, that schools would introduce work changes which have a further negative impact on teachers’ working lives.
"This smacks of crisis opportunism and cannot go unchallenged."
The ASTI ballot will also cover the difficulties faced by returning teachers.
