Only around one-in-four healthcare workers in hospitals availed of a flu jab, which is aimed at preventing the spread of the disease to vulnerable patients.
The HSE offers the vaccine free of charge to staff in hospitals it funds, nursing homes and other disability facilities.
The Health Protection Surveillance Centre (HPSC) conducted a survey to find the level of uptake among workers. It found that during the 2013-14 influenza season, the overall uptake among hospital staff was nearly 25pc, and it was slightly lower for those working in long-term care facilities, at nearly 23pc.
"The take up is far too low," said Stephen McMahon, CEO of the Irish Patients Association (IPA). "It's creating far too many risks for themselves and for the patients.
"I would encourage all healthcare workers to avail of the opportunity to protect themselves, their families and patients from the flu," he added.
In addition, he said that he believed that absenteeism policies must be looked at.
"I have been informed of an incidence where if a healthcare professional is out sick, they have to physically deliver their doctor's cert by hand back into the hospital. They can't send it in by third party."
He added that he did not know if this was a widespread practice.
Meanwhile, the HPSC figures showed that at national level, the uptake of the vaccine varied amongst the various staff categories, and was highest in the "medical and dental" professionals group.
However, the figures were up overall, with just 17pc of hospital staff availing of the vaccine in the previous flu season.
In hospitals, the highest uptake was reported in the Dublin North East region.
"The HSE recommends that all health care workers in Irish health services receive the seasonal influenza vaccination each year," the report from the HPSC said.
It said that achieving a high uptake of flu vaccination is recognised as an important infection control intervention and occupational health issue, to reduce the risk of flu transmission between patients and healthcare workers "with the potential for severe disease in patients and staff".
The report said that between January and April of this year, 56 flu-related general outbreaks in healthcare settings, including hospitals and residential units, were notified in Ireland.
"Some progress has been made compared to the previous seasons," the report noted.
It said that nearly 34pc of those working as medical and dental professionals in hospitals got the vaccine, compared to 18pc of nurses.
However, there was a 6pc hike in the number of nursing professionals being vaccinated against the flu, according to the national disease watchdog.