HIQA inspectors say hygiene standards at the National Maternity Hospital's delivery ward are very poor.
In an unannounced inspection of Holles Street last October, they found evidence of organic contamination on surfaces including equipment.
In a new report published this morning, HIQA says management said high levels of activity recently had made it difficult to access the delivery ward for cleaning - which was disputed by inspectors.
Concern has also been raised about the storage of syringes, and medicines being left out for long periods of time.
The report states that hospital officials acknowledged overcrowding in the neonatal intensive care unit, and suggested it cannot be mitigated due to current space restrictions at the hospital.
A second inspection was carried out in November. HIQA said that while a 'commitment to addressing immediate high risks was evident', improvements were still needed.
HIQA says that, "notwithstanding the infrastructural challenges in the National Maternity Hospital, an issue shared with other older hospitals, an acceptable standard of basic cleanliness and maintenance is both essential and achievable.
"Improvements are required relating to cleaning processes, resources and the oversight of hospital hygiene. Older and poorly designed hospital infrastructure is more difficult to clean, this needs to be taken into consideration when allocating cleaning resources," the report adds.
The agency also says that overcrowding issues need to be effectively managed during the planning and building of a new dedicated maternity hospital over the coming years.
Paul Cullen, Health Correspondent with The Irish Times, spoke to Lunchtime about the report, observing "the National Maternity Hospital is a very old building... it's a very difficult environment. But HIQA is not stepping back from its very serious recommendations here":