The cases of people hospitalised with flu is expected to almost double in the next ten days.
A senior HSE spokesperson has said there could be 800-900 cases of flu in hospitals in the week at the end of the year with a peak expected in January.
Dr Colm Henry, the HSE's Chief Clinical Officer, has said there are more than 525 patients in hospital with flu, and 155 patients with RSV.
It is driving increased pressure on the healthcare system, he said.
"The real driver for increased activity and pressure throughout our healthcare system, not just on hospitals, is the rise in flu cases and we expect this to continue to rise until the end of the year at the very earliest."
He said based on previous years, the cases are expected to continue to rise and spike as people return to work in January and children return to school.
Dr Henry reminded people it is not too late to get the flu vaccine as it will be effective two weeks after people take it and it can reduce the amount of people who may get sick with the illness.
He said a peak of 800-900 cases of hospitalisations with flu will be by the end of the year, but that an increased pressure on hospitals and on primary care settings will be expected throughout the month of January.
He said the HSE has been preparing and planning as Emergency Departments already have a high level of pressure on them.
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It comes as a consultant in emergency medicine said the coming weeks are going to be very difficult for hospitals as the flu season peaks.
Speaking on RTÉ's Brendan O'Connor, Dr Emily O'Conor, said "we are looking at it hitting us in the next two weeks, which from the point of view of hospitals and GPs; they are difficult times of the year, staffing wise etc to actually accommodate a flu peak."
Dr O'Conor said there was some good news in terms of the introduction of the RSV vaccination for newborn babies which began this year.
She said it had "changed this bronchiolitis season; there has been a huge reduction in the numbers of babies being admitted to hospital with bronchiolitis".
Dr O'Conor said previously there would have been "significant numbers of babies being required for oxygen and feeding because of bronchiolitis".
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Dr Colm Henry said there have been 73 cases of RSV so far this year compared to over 800 last year, while there were 35 hospitalisations with RSV this year compared to over 500 last year.
There were 70 cases admitted to ICU with the virus last year while so far, only seven this year.
He said this was down to the "remarkable impact of the campaign" to vaccinate newborn babies from RSV.
'Crucial' to get flu vaccine, says pharmacy union president
Flu vaccines are "readily available" over the next two days at pharmacies around the country.
The President of the Irish Pharmacy Union said that people can telephone ahead to get an appointment for a flu vaccination.
Tom Murray said although pharmacies are busy with prescriptions and Christmas business, most of them will open tomorrow and for a few hours on Christmas Eve.
"It is crucial that members of the public get the flu vaccine, not just to protect themselves but everyone else too."
Mr Murray said the vaccine, a nasal spray for children and injection for adults, takes two weeks to kick in "for the body to generate the full antibody content to protect you against flu".
But he said as the peak is yet to come, it is important to be protected against this season's flu.
He said pharmacies are feeling the pressure: "We are under a lot of pressure. There is always a increase in the volume of prescriptions, at this time of year."
