BCG vaccines which are given to babies to protect against tuberculosis (TB) will remain out of stock until late July at the earliest.
Concerns have been raised at the ongoing postponement of BCG vaccination clinics in HSE centres and maternity hospitals.
The shortages were raised with Health Minister Leo Varadkar in the Dail by Independent TD Michael Healy-Rae.
"I was contacted by constituents and people from the medical profession about the matter. Any time a vaccine is scarce like this, usually it's only the right thing to raise it," he told the Herald.
In his response, Mr Varadkar said the BCG vaccine is currently part of the primary childhood immunisation schedule. It is given to prevent the most serious forms of tuberculosis in children, such as TB meningitis.
"The HSE is in close contact with the vaccine manufacturer to expedite delivery of new stock as soon as possible, and local health centres will arrange appointments for BCG vaccination clinics when the BCG vaccine supply is restored," Mr Varadkar said.
"There is no threat to public health from this temporary vaccine shortage," he said.
The HSE said that it is currently experiencing delays with the supply of BCG vaccine, which is a European-wide issue.
"There is only one licensed manufacturer of BCG vaccine in the EU. This vaccine manufacturer has informed us that the BCG vaccine will not be delivered into Ireland until late July at the earliest.
"The BCG vaccine stock in all areas expired at the end of April, so BCG vaccination clinics in HSE clinics and maternity hospitals have been postponed until new stock arrives," it said.
"In Ireland, the number of cases of TB has been falling and there were no cases in young children in 2014.
"Most European countries do not give BCG to all babies," the HSE added.