The proportion of children receiving the MMR vaccine has fallen to an "alarming" extent, according to the National Disease Surveillance Centre.
There has also been a fall in the take-up of all other vaccines except the new meningitis C vaccine.
The fall has occurred in all regions of the State and is a cause for serious concern, the NDSC says.
The biggest fall has been in the take-up of the three-in-one measles-mumps-rubella (MMR) vaccine, according to an article by Dr Margaret Fitzgerald and Dr Darina O'Flanagan published in the current NDSC bulletin EPI-INSIGHT.
The diseases which the vaccines protect against are diphtheria, whooping cough, tetanus, HIB B (a cause of meningitis), polio and MMR.
According to Dr Fitzgerald and Dr O'Flanagan there are three possible reasons for the decline.
One is that children have to be taken for three separate doses for the diseases other than MMR.
New four-in-one and five-in-one vaccines for these diseases should help address this problem, they write.
Another is the announcement in December that a British blood donor, who contributed a stabilising agent used in the manufacture of oral polio vaccine, had developed CJD.
Experts said that the risk of contracting CJD from the vaccine was "essentially non-existent".
However, the authors of the article feel the publicity may nevertheless have put some people off having their children vaccinated.
A third possible cause for the fall is the "ongoing media attention to alleged vaccine adverse events from MMR vaccine".
They point out that the Joint Oireachtas Committee on Health and Children found no evidence of a proven link between MMR and autism.
In the first quarter of this year, only 80 per cent of two-year-olds had been immunised against MMR compared to 83 per cent in the last quarter of 2000.
Of the eight health regions, five had a take-up below 80 per cent for MMR compared to the more than 90 per cent which is considered desirable.
Last year only the South Eastern Health Board had exceeded the 90 per cent target with a take-up of 92 per cent among two-year-olds, but that figure fell to 90 per cent this year.
These figures compare with a take-up of 91 per cent in Northern Ireland and Scotland.
Earlier this year it was announced that measles was no longer being transmitted in Northern Ireland.
Last year there was only one confirmed case of measles there compared with 1,600 in the Republic, where two children died.
Making the announcement Dr Richard Smithson, chairman of the Independent Expert Advisory Group on Vaccinations, pointed to the situation in the Republic as warning of what could happen if there was a low take-up of the MMR vaccination.
In their article, Dr Fitzgerald and Dr O'Flanagan say: "Childhood vaccinations have had a major impact on the reduction and elimination of many causes of morbidity and mortality among children.
"Babies are very susceptible to measles, mumps and rubella which are killer diseases, so they must be protected as soon as possible.
"This can only be done with the MMR vaccine."
They reject calls from some parents for the MMR vaccine to be given as three separate vaccinations, saying this would leave children unnecessarily exposed and vulnerable.
pomorain@irish-times.ie