The Irish Society for Autism says it has been "experiencing some difficulty in achieving regulation with HIQA"
Three centres for people with autism have been taken over by the HSE at the request of the health watchdog.
The Health Information and Quality Authority (HIQA) had significant concerns for the care and welfare of almost 50 residents at the three centres run by the Irish Society for Autism.
The centres taken over by the HSE are Cluain Farm and Dunfirth Farm in Co Meath, as well as Sarshill House in Co Wexford.
The watchdog had increased monitoring at the centres and issued warning letters.
However, the situation did not improve sufficiently, and the centres had their registration withdrawn.
The society says it has been experiencing difficulty achieving regulation with HIQA and that it hopes the arrangement with the HSE will ensure the services can continue.
In a statement, the society said: "We are a small organisation and we believe that, in the long term, this decision is in the best interest of our residents. We are very grateful to all for their commitment and perseverance during this difficult period."
Responding to the news, Sinn Féin TD Caoimhghín Ó Caoláin said: “These adults with special needs and their families require and deserve the highest standard of care.
"To hear of such non-compliances is extremely distressing and requires immediate address by the HSE," he added.