The HSE is to spend €1.1m on extended security support for a now obsolete operating system as the health service did not upgrade the majority of its computers in time.
Security support for the Windows 7 system is due to expire next week, a deadline that has been repeatedly flagged by the tech firm over the last five years.
Organisations still using the system must now pay for extended support from Microsoft or put themselves at risk of cyberattacks.
While a programme to update HSE devices to Windows 10 began in 2017, many of the health-specific applications used required extensive testing, according to the HSE.
The health service has 46,000 Windows 7 devices on its network, out of 58,000 Windows devices, a spokeswoman confirmed.
Microsoft offered the health service support through its extended security update programme in November, she added.
"Negotiations were carried out with Microsoft in order to achieve the best value for money for this service. The cost is approximately €1.1m for Windows 7. It was decided by the executive management team to avail of this extended support."
Almost 80% of 58,000 HSE Windows devices still use the system, with 34,000 of these currently on "an accelerated upgrade programme".
However, about 12,000 devices cannot be replaced until the HSE Radiology Information Systems are upgraded in 2021.
The HSE has more than 6,000 locations nationally that use Windows 7 devices, the spokeswoman added. "This makes the size and scale of the upgrade logistically and technically challenging.
The initial deployment of Windows 10 devices was slow and methodical to ensure that patient care would not be compromised by the upgrade.
"During 2019 the HSE deployed 12,000 devices across a range of locations and services and we are now confident that we can begin to deploy at pace in 2020 utilising a standard Windows 10 build."
In an average year, the HSE would replace about 7,500 desktops and laptops. "This equates to a replacement of each device every 7 to 8 years."
"In 2020 the plan is to increase this number to a total of 13,500 devices, by bringing forward those devices due for replacement in 2021 by one year, as upgrading these in 2020 would not be value for money."
The HSE annual IT budget for new and replacement devices is to be increased by €5m to €11m this year in order to replace devices, she added.
"In addition, we will spend €2.5m in upgrading Windows 7 devices which can support Windows 10, in 2020, which is less costly than purchasing new systems. The balance of device upgrades will be completed in 2021 at a cost of €2.5m."
Meanwhile, the Department of Education has no record of the number of schools who may be affected by the ending of security support to Windows 7.
A spokesman for the department said it has no role in advising schools to update operating systems, and would not issue a circular directing them to do so.
"Each manufacturer, reseller or provider of such services to schools would be expected to apprise schools of any such requirements in the context of their contractual obligations to the school."