Parents are being advised to keep sick kids at home next week as the winter flu strain is affecting children from babies up to 15-year-old teenagers.
Fewer than 10 people have died of flu so far this winter, but the HSE would not say if that included children due to confidentiality.
At least 190 people have been hospitalised with flu, but that figure will rise as figures are sent back to authorities.
It comes as hundreds of patients are waiting for beds in hospitals across the country.
Dr Kevin Kelleher of the HSE says anyone with flu-like symptoms - which include sore throat, fever and muscle ache - should stay at home.
He stated: "The issue is that we want to make sure it's not spread.
"Going back to work when you've got symptoms or going to school when you've got symptoms will spread it. Flu spreads very easily, particularly in closed [areas] like a classroom or workplace."
He added: "If your child has the symptoms, please don't send them into school - look after them at home. Likewise, if you've got the symptoms, don't go into work."
The call was echoed by Health Minister Simon Harris.
He explained: "I am worried about the spread of the flu when kids go back to school.
"We're seeing a strain of flu that is affecting children this year we didn't see last year. I would advise parents, if your child is under the weather, please keep them home from school next week."
He stressed: "It is important if you have the flu in general, try not to spread it: stay at home; take advice on undertheweather.ie; consult your pharmacist and GP - don't just go to the ED, unless advised to do so my a medical professional."