The Department of Health said it shut down its IT systems after a ransomware attack on Thursday.
A similar attack on the Health Service Executive (HSE) on Friday caused “substantial” cancellations to outpatient services.
The same cyber-crime group is believed to be behind both incidents, RTÉ has reported.
It is not believed to be espionage.
Ireland’s health department said it was still assessing the impact on its systems, according to RTÉ.
Vaccines going ahead
The attack on the HSE has been described as the most significant in the state’s history.
The Covid-19 vaccine portal was forced to close temporarily on Friday but authorities have said the programme will continue as planned with about a quarter of a million doses expected to be given in the next week.
However, officials said the attack has caused “substantial cancellations across outpatient services”.
It is expected to be a few days before the system is fully restored.
Irish Foreign Minister Simon Coveney said malware had been inserted across the HSE healthcare system network “in multiple locations”.
“It’s going to take quite some time, I understand, to clean that data, piece by piece and to try to backup and protect as much of the data as we can – so this is a very serious attack.”
On Saturday, Ireland’s health minister, Stephen Donnelly, said the impact across the country “will vary” due to the data kept by hospitals, but warned there would be “cancellations in the coming days”.