Letterkenny University Hospital is the worst affected in the country today with 43 people waiting for a bed.
The centre has been at crisis-point in recent days due to a number of people being hit by an outbreak of flu.
Meanwhile, HIQA said it does not have the power to regulate acute general hospitals and has no enforcement powers.
HIQA said it can conduct investigations, at the direction of the Minister for Health, under Section 9 of the Health Act 2007, or on the direction of the Board of HIQA.
The watchdog said that in recent years, it had assessed the quality and safety of a number of emergency departments including at Tallaght, Limerick and Portlaoise.
“These findings and recommendations had implications for services locally and nationally”, it said.
The Tallaght probe was initiated by the HQA Board.
HIQA added that the responsibility for compliance with standards rests with the provider of the services – the Health Service Executive or the voluntary hospital, and those charged with making policy, the Department of Health.
RTE is reporting that HIQA said that the regulatory system in Ireland “varies significantly” to those in place in other countries regarding reach, monitoring and enforcement.
“The current programme, as funded by the Department of Health, merely allows for targeted monitoring in high-risk areas”, it added.
These areas include medication safety, antibiotic resistance, infection prevention and nutrition and hydration care.
HIQA says it has the power to monitor public acute hospitals, against nationally mandated standards and these are publicly reported on.
Its 2012 statutory investigation report into the emergency department at Tallaght Hospital, criticised the hospital saying patients’ lives were being put at risk because they were being treated on trolleys in corridors.
That report said that all hospitals should stop using hospital corridors, or parking areas for trolleys, to accommodate patients receiving clinical care.
It also suggested that no patient should spend more than six hours in an emergency department.
Earlier, SIPTU called for HIQA to get involved in efforts to solve the overcrowding crisis.
SIPTU Health Division Organiser Paul Bell said its members are working in unsafe conditions because of consistent pressure on the health service.
Mr Bell said HIQA was an independent agency, which was set up to investigate such matters.
It comes as the Irish Nurses and Midwives Organisation said there are 551 patients on trolleys in emergency departments, or on wards, waiting for a bed.
The number is down from the 575 patients it recorded yesterday.
The hospital worst affected is Letterkenny General Hospital with 43 people waiting.
Health Service Executive figures show there are 420 patients waiting on trolleys in emergency departments.
The number is down slightly on yesterday’s figure, however, there are 57 patients waiting over 24 hours, which is higher than yesterday.
The hospitals worst affected are University Hospital Galway with 42 people waiting, Mercy University Hospital in Cork with 32 waiting and Tallaght Hospital with 30 people waiting.
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