The warning comes after it was revealed that the National Public Health Emergency Team (Nphet) will consider compulsory vaccination for health staff and has asked officials to provide a report for upcoming meetings.
However, Tony Fitzpatrick of the National Joint Council of the Health Sector Trade Unions said they would oppose any such move.
"It does not make sense. The majority already have the vaccine. We object to mandatory vaccination but have done the reasonable thing and encouraged everyone to take it up," he said.
Around 300,000 health staff are in line for booster shots, he pointed out.
Unions agreed to a risk assessment where a worker who is unvaccinated and a potential risk is redeployed to a non patient-facing job.
The HSE has no figures on how many staff are not vaccinated but said "all the indications are that there is a very high uptake" of the Covid jab.
At its November 11 meeting, members of Nphet referred to mandatory vaccination of healthcare workers in other countries. The meeting noted the complexities surrounding the practice.
It decided that relevant ethical, legal, and practical issues should be thoroughly examined before any action is considered. The Department of Health will prepare an evidence paper on the topic for consideration at a future meeting.
The potential crackdown comes as other countries get tough, including England which has signalled a compulsory vaccination rule for the NHS could be enforced by next April. The proposal has met with a lukewarm response in Northern Ireland.
In the week to November 22, some 33 patients and 35 staff here picked up the virus in a healthcare setting. But this could be due to various sources, including fully vaccinated people who are at risk of getting Covid-19 and passing it on.
The HSE can ask a member of staff if they are vaccinated and can then risk assess if they pose a risk to patients, moving them to other lower-risk areas.
The Forsa trade union insisted that the vaccination rate among healthcare workers is very high and it actively urged its members to avail of the jab.
A spokesman said they would continue to talk to the HSE and wait for the outcome of Nphet discussions.
The Irish Nurses and Midwives Organisation said it had actively called for a booster jab for healthcare workers.
"It is notable that Nphet also looked at ventilation measures to improve air quality at the same meeting. Many of our hospitals have issues with air quality and ventilation which we raised with the HSE and the Health and Safety Authority.
"Hospitals are not just care settings but places of work," said a spokeswoman for the nurses' union.
Hospital groups for the most part were unable to account yesterday for how they manage the patient safety issue of protecting vulnerable people in their care if staff choose not to be vaccinated.
Several groups including the South and South West Group, as well as the Dublin Midlands Group, were unable to say what safety measures they have in place.
The Saolta Hospital Group, covering the west and north west, was the only one to be publicly accountable on how it is protecting patient safety, saying there has been a significant demand to receive a Covid-19 vaccine to date among its staff and all indications are that there is a high take-up.
"There is a policy in place to address situations where staff in critical roles are unvaccinated which is managed at local level and we know this is a relatively small number.
"Around 3pc of staff in the group who said they were unvaccinated or wished not to disclose their status have been assessed to determine if they be redeployed."
A Government source indicated reluctance for a compulsory mandate.