The Kerry Parents and Friends Association say they have been ravaged by six years of funding cuts.
Two HIQA inspections found deficiencies with regard to fire safety in two of the centres for adults with learning disabilities.
CEO Marie Linehan admits there were issues found relating to fire safety measures in both Listowel and Killarney.
However, she says some of the older centres have suffered due to cuts in funding in recent years.
She says €250,000 would be needed for improvement works.
The state watchdog also reported insufficient measures were in place to safeguard residents with learning disabilities, as well as highlighting an alleged instance of non-sexual abuse in Listowel.
Marie Linehan says she took the allegation very seriously, and while she could not comment on the case, there was no need to involve the Gardaí.
She adds Kerry Parents and Friends Association had already notified the HSE of the matter prior to the HIQA inspection.
The report says the plan submitted by the Kerry Parents and Friends in response to the allegation was robust and adequate.
However, it was not acted upon within the recommended three-day timeframe.
Marie Linehan says it was simply a matter of not meeting the deadline.