The Health Minister has cast doubt over the promise to have 80% of adults vaccinated by the end of June.
The National Immunisation Advisory Committee (NIAC) is due to issue guidance on what age groups should be given the AstraZeneca vaccine following blood clot concerns in younger people.
The European Medicines Agency (EMA) last week confirmed a link between the vaccine and very rare blood clots, but stressed the benefits of the vaccine outweigh the risks.
However, several countries are still rethinking their vaccine strategies as a result, wth under-55s in France set to be offered an alternative.
Stephen Donnelly said the cornerstone of the vaccine programme is a "safety first" approach, and if operational changes are recommended, the Government will accept them.
A number of other countries have already rowed back on the AstraZeneca vaccine and are now only giving it to older groups.
Asked specifically if he can still commit to having 80% offered a jab by June, Mr Donnelly said: "We have to wait to see what NIAC says in terms of any potential operations for the programme."
Mr Donnelly also said it is "only natural" to see a spike in people arriving here in the coming days to avoid hotel quarantine
France, the US, and Italy are among 16 countries due to be added to the mandatory quarantining list from Thursday.
Mr Donnelly said: "The intention of the gap is really to give people the opportunity to book into mandatory hotel quarantine. Inevitably, if you have a gap between when you announced the country will be on a category two list, and when you go live with that a few days later, there will be people who look to get in ahead of that, that's perfectly natural that they would.
"We are very concerned and indeed public health are very concerned about the high rate of variants in those countries."
However, he added that "in the main" it is expected that the number of people arriving here from countries on the list will decrease significantly.
Mr Donnelly said at some point, capping the number of people who enter the country may be needed if hotel capacity comes under pressure.
He said hotel quarantining accommodation has been projected based on an 80% reduction in travel.
"It is the case though, as with the New Zealand system, the Australian system, and other quarantine systems, that you may not in all cases be able to have a room allocated on every single day that you may want," Mr Donnelly told RTÉ'sprogramme.