Over 46,000 of the HSE's 58,000 laptops and desktops are operating on old software, with the body spending over €300,000 patching it up, RTÉ News has learned.
This comes as Microsoft will stop protecting Windows 7 from viruses and malware from 14 January next year - except for those who pay a new premium for extended security support.
Over 22,000 computers in various government departments and offices also continue to run on Windows 7.
The information was released in a series of Parliamentary Questions to many government departments by Labour TD Alan Kelly.
"Across government, across departments and various organisations there is a lack of preparedness, in some cases, for the change over from Windows 7 to Windows 10. As a result it is going to cost the taxpayer a substantial amount of money", he said.
"This is something we should be very much worried about. There obviously hasn't been a cross government policy in relation to this," he added.
"When you have that level of risk in the HSE - the largest public sector organisation in the country - an organisation that has very sensitive data in relation to almost every citizen in this country then this is worrying", said Mr Kelly.
He also said he is very concerned about possible cyber attacks.
Barry Lowry, Government Chief Information Officer at the Department of Public Expenditure, said there is enough security in place in departments to protect systems and peoples' data.
Goverment has "plans in place which are being actioned" to deal with Window 7 issues, says Government Chief Information Officer Barry Lowry. pic.twitter.com/hL8Hn9yc2x— cian mccormack (@cian_mccormack) November 14, 2019
"Devices don't suddenly become unprotected in January 2020. The option is there to take out Microsoft security support through 2020 and further," said Mr Lowry.
"The IT departments within the various departments are carrying out refresh programmes and also have security programmes in place.
"I'm pretty confident that technically we are in a good position," Mr Lowry added.
The HSE said in a statement that "the protection of personal data is a top priority" and it "uses layered security to protect data from hackers and malware".
It said it has an "accelerated refresh programme" to address the Windows 7 issue and expects this work to be finished within the calendar year - with the exception of a number devices.
Some of its health systems do not run on Windows 10.
As Windows 7 is phased out there are 22,000 government computers and 46,000 HSE computers running on it. There is concern. pic.twitter.com/NyNI2SXqPM— cian mccormack (@cian_mccormack) November 14, 2019
It added it continuously is replacing and updating older systems. Costs are built in to current budgets and future costs depend on priorities and available budgets.
The HSE has paid €330,000 for an extended warranty to protect 16,000 Windows 7 computers and 46,000 of the HSE's 58,000 desktop and laptop computers remain on the Windows 7 operating system.
The HSE said Microsoft offered it extended security updates last Tuesday, but there was no financial proposal with that offer.
It said it is not in a position to comment because Microsoft pricing fees for extended support have not yet been released.
However, there are agreements with other government departments.
The Department of Public Expenditure is paying Microsoft €48 per computer for extended warranties on 398 until the end of 2020 - at a cost of about €20,000.
The pricing structure has not been confirmed by Microsoft.
However, industry and government sources say it is around €50 per device for the first 12 months, then double that for the next 12 months, and double that again for the remaining 12 months.
This means an organisation with 1,000 PCs on Windows 7 could possibly face a fee of €50,000 in 2020, rising to €200,000 in 2022.
But some organisations may get better pricing if they have large numbers of Windows 7 computers.
Initial figures released to Mr Kelly show there are 22,312 computers across various government departments and offices running on Windows 7.
There has been a proactive drive within government departments and offices to get computer systems updated.
The Department of Justice has 3,700 computers operating on Windows 7.
The Department of Agriculture, Food and Marine has 2,950.
The Department of the Taoiseach has one.
The Department of Finance has 269.
The National Services Office has 797.
The Department of Housing, Planning and Local Government has 82.
The Department of Education has 450.
The Department of Foreign Affairs has 1,320.
The Department of Communications, Climate Action and Environment has 552.
There are 11,010 in the Department of Employment Affairs and Social Protection.
The Department of Transport, Tourism and Sport has 605.
The Department of Culture, Heritage and the Gaeltacht has 16.
The Department of Defence has 480
The Department of Health has 4.
The Department of Children and Youth Affairs has 290.
The Department of Rural and Community Affairs has 131.