His comments come amid concerns that the Lambda variant of Covid-19 discovered in Peru may be more resistant to vaccines than other strains such as Delta.
Professor Luke O'Neill has said that there is a possibility a "nasty variant" could send the vaccine programme "back to square one".
O'Neill said that he would urge countries to postpone vaccinating younger cohorts in order to vaccinate developing countries to help slow the spread of new variants.
"There's a remote chance of a nasty variant emerging that'll break through everything and then we'll go back to square one," he told Newstalk's
The Pat Kenny Show on Thursday.
"That's our last remaining scientific worry, in a way.
"This is why we shouldn't vaccinate the under-12s in my opinion at the moment, give the vaccine away to developing countries to stop variants.
"Our biggest concern is new variants really, to stop it, and it's running rampant in all these countries.
"So just in case a nasty variant crops up we've got to prepare, in a way, for that and try to mitigate against it by getting widespread, global vaccination."
O'Neill added that he believes countries such as Ireland should donate vaccines to developing countries in order to help prevent new variants from emerging.
"That makes sense to me because we don't want these variants cropping up," he said.
The HSE has said it will likely rollout a booster vaccination programme to enhance the protection of the vaccine against Covid-19.
However, the World Health Organisation (WHO) has asked countries to suspend any booster programmes until at least September to allow developing countries to be vaccinated.
It comes amid concerns a Lambda variant of Covid-19 discovered in Peru may be more resistant to the Covid-19 vaccine than other strains such as Delta.
The variant which was first identified in Peru and is now spreading in South America is highly infectious and more resistant to vaccines Japanese researchers have found.
After conducting laboratory experiments, they found that three mutations present in Lambda's spike protein, known as RSYLTPGD246-253N, 260 L452Q and F490S, help it resist neutralization by vaccine-induced antibodies.
Two additional mutations, T76I and L452Q, help make the Lambda variant highly infectious, they found.
In a paper posted on Wednesday on the researchers warned that due to the variant being labeled a "variant of interest" and not a "variant of concern" by WHO, people may not realise the seriousness of its threat.
