The HSE has written to Alcoholics Anonymous over a meeting the health service alleged contravened Covid-19 guidelines.
Health chiefs claimed they were aware of a meeting that breached regulations on numbers attending, the wearing of face masks and social distancing.
In a letter dated August 25, officials said they were concerned that more than six people attended, contrary to the tightened restrictions imposed last month as coronavirus infections rose.
Now dozens of AA groups, which only resumed face-to-face operations last month after a six-month suspension, have again voluntarily suspended meetings.
They will continue via online platforms such as Zoom.
The majority of AA and Narcotics Anonymous (NA) groups went to great lengths to try to adhere to HSE guidelines.
They insisted all attending should wear face masks, off-ered contact tracing details and adhered to social distancing and sanitisation measures.
However, compliance with the six-person rule for indoor gatherings emerged as an issue.
The AA general service office has written to Health Minister Stephen Donnelly asking for urgent clarification.
"This letter should serve to remind us of the seriousness of the pandemic while highlighting the reputational risks to the good name and work carried out by AA in Ireland," it said.
"We should always be conscious of our responsibility to others inside and outside of AA."
Politicians have expressed concern that groups providing an essential service, such as AA and Narcotics Anonymous, could now effectively be forced to shut down at a time when revellers have been seen flouting Covid controls in Dublin and Killarney.
Politicians said AA groups adhering to guidelines such as face masks, social distancing, contact tracing and sanitisation should be deemed an essential service and exempted from the six-person rule brought in to tackle the pandemic.
Several warned there could be serious mental-health consequences over the loss of such services for a prolonged period.
Sinn Féin deputy Thomas Gould expressed concern at the move and asked why AA and NA meetings have not been deemed essential.
"For some people, these meetings are a lifeline to help them retain their sobriety," said the Cork north-central TD.
"These meetings are controlled environments where contact tracing, social distancing and risk management is possible. If clusters have arisen from these meetings, they must be stopped, but we have no information on that.
"These are well-run and well-managed organisations that I would trust to put their members first and do everything in their power to keep society safe while still providing the support necessary to those struggling with past problematic alcohol and drug misuse during this pandemic."