Special needs campaigners have called the drugging of autism patients a "fundamental abuse of human rights".
The health authority has revealed it has taken over the running of three residential centres for adults with autism, because they were using drugs to chemically restrain patients.
The complaint is part of a litany of failures found at three residential homes run by the Irish Society for Autism.
Forty-seven adults with autism appear to have been failed by the system set up specifically to care for them.
They were living in residential centres at Cluain Farm in Westmeath, Dunfirth Farm in Kildare, and Sarshill House in Co Wexford.
All three homes had been run by the Irish Society for Autism until serious problems were caught by the health watchdog, HIQA.
Over the last 18 months, HIQA inspections found that residents were traumatised, living in fear and constantly assaulted by other patients.
Residents were engaging in self-harm, leaving without being spotted and having their dietary requirements unmet.
Staff were untrained and facilities were underfunded.
But arguably the worst allegation of all concerns the use of medication to control disruptive residents.
Anti-psychotic drugs, sedatives and pain killers were all fed to patients to quieten them.
The charity admitted it has been experiencing “some difficulty in achieving regulation with HIQA”.
It added: “These have been very challenging times for all concerned including our residents and staff, many of whom have been with us for a long time.”
Despite initial objections to two of the takeovers, which were later dropped, the charity said: “We are a small organisation and we believe that, in the long term, this decision is in the best interest of our residents.”