The HSE CEO Paul Reid says there's "no doubt" more people are now testing positive for COVID-19 while in hospital for other reasons.
However, he said such cases do still put a significant burden on the hospital system due to the need for COVID specific care and isolation.
The number of patients in hospital with the virus has increased again today to 884, an increase of 80 compared to yesterday.
Staff absences are now also having a significant impact on many healthcare settings, with some hospitals reporting more than 200 frontline staff off work as either close contacts or confirmed COVID-19 cases.
One question around the hospitalisations figure is how many patients are in hospital for COVID specifically, and how many have tested positive while in hospital for other reasons.
Mr Reid told The Pat Kenny Show that typically around 90% of COVID-19 patients in hospital are being primarily treated for the virus itself.
However, he said that percentage has likely changed over the last week or two - noting that full data is being put together at the moment.
He explained: “We would track on a weekly basis COVID admissions, and then those others who are admitted for other legitimate health reasons and then identified as COVID while in hospital.
“There’s no doubt over the last ten days that the number who have come in with other illnesses and been identified as COVID has increased.
“I do think it’s important to say that once people are in hospital and having identified as being COVID… they still do need the supports and monitoring. It's consistent for all patients."
He said such patients do still need to be isolated from others, while COVID-19 can have a particularly severe impact for those who do have other illnesses or underlying conditions as well.
He also noted that while early indications are that Omicron causes less severe illness than previous variants, it will still take 5-7 days to see how the recent rise in hospitalisations will translate to ICU admissions.
The five-day moving average of new COVID-19 cases has neared 20,000 in recent days, amid high levels of Omicron transmission in the community.
With the testing pressure under significant demand and positivity rates in excess of 40-50% in recent days, Mr Reid said it's clear there are more cases out there than the daily figures capture.
He said: “It’s probably much higher than what we’re seeing in the daily cases.”
The HSE IT team is currently looking at ways of recording antigen test results - with Mr Reid saying that does require a bit of work as the system is currently designed ‘end-to-end’ around PCR tests.
Meanwhile, Mr Reid has written a letter to the country's hospital groups which he says "gives clarity" that the focus should be on urgent care and COVID care over the next 14 days.
That means elective care can be “scaled down” where necessary, while private hospital capacity is also being used “to the greatest extent we possibly can”.
The HSE CEO noted: “Hospitals would have been taking these decisions anyway, but it’s setting out to give a level of consistency and direction at a national level.”
While the letter covers the next two weeks, Mr Reid said there's still uncertainty over the trajectory of the virus and the situation will be reviewed regularly.