The research was carried out by Dr Coilin O hAiseadha, a specialist registrar in public health medicine, who sent out questionnaires between April and June to a random sample of more than 1,064 HSE staff across the country.
He had a response rate of some 71pc.
He found that there were significant variances in prevalence between different staff categories, with up to 25pc of general support staff still smoking, compared with 4pc of medics.
Dr O hAiseadha said that it was nonetheless a good sign that that there were now more ex-smokers in the HSE than current smokers.
"The overall proportion of ex-smokers was 27pc, so for every current smoker, there are almost two who have successfully quit," he said.
And the research found that an overwhelming 81pc of smokers said that they would like to give it up.
Overall, nearly half (48pc) had tried to quit in the 12 months before the audit.
The research recommended that the HSE should ensure that all front-line staff, especially doctors, are aware of its quit services.
There were also significant differences regarding awareness of the HSE's health education campaign, which highlighted that one in every two smokers will die of a tobacco-related disease, with only half of medical and dental staff being aware of this.
Dr O hAiseadha's research was assisted by Marie Killeen of the National Tobacco Control Office and Dr Fenton Howell of the Clinical Strategy and Programmes Directorate.
It was presented at the Faculty of Public Health Medicine's 2012 Winter Scientific meeting at the Royal College of Physicians of Ireland.
Overall, there are about 1m smokers in Ireland and, each year, some 5,500 people die of a tobacco-related disease.
It is estimated that €1-2bn is spent each year by the HSE in treating tobacco-related diseases.