SIPTU says staff at St. Anne's Centre in Tipperary should have been given a right of reply before a HIQA report was published.
The trade union said it is disappointed with the publication of the report into the centre for people with intellectual disabilities in Roscrea.
The Health Information and Quality Authority has carried out a number of inspections and said residents were not treated with dignity during an unannounced inspection.
SIPTU Organiser Mark Lohan said that despite the disagreement over publication, staff will co-operate with HIQA.
"There have been several HIQA investigations this year that have raised some concerns - and SIPTU members will cooperate fully with any outcome," he said.
"What is paramount in this for our members who are the frontline staff taking care of vulnerable service users is [patient] safety and welfare."