Just one in four under-12s have been registered for a COVID-19 vaccine so far.
New figures seen by Newstalk show a reluctance among parents to have their children take the vaccine - with the number of new registrations dropping sharply over the last two weeks.
Only 12.5% of five to 11 year olds are double vaccinated, with 22.6% having been given a single dose.
The HSE estimates that over 100,000 children who got the virus over Christmas may now be eligible for their vaccine.
Dr Lucy Jessop is director of public health at the National Immunisation Office.
She says they were expecting the take-up among children to be slower.
"Parents have told us that they need time to think about whether they are going to bring their children forward for vaccination.
"So we want to give them plenty of time, and we want to give them all the information that they need to make that decision.
"So I think it's partly around time - it's also, obviously we know, just before Christmas there were a lot of children that were infected with COVID unfortunately".
It comes as laws around the use of face masks in shops, schools and on public transport are expected to be dropped and replaced with guidance.
Liam Fanning, professor of immunovirology at UCC, earlier told Newstalk Breakfast the vaccine gap is concerning.
"The latest data would indicate that only about 55/56,000 have their second dose.
"Now lots of them wouldn't have got their second dose because of being infected over the Christmas period.
"Their parents should ensure that they get the second dose three months after their infection.
"This is about the now, but also about future protection".
Additional reporting: Jack Quann