The authority apologised for any inconvenience to patients and the public but said its COVID-19 vaccination programme and the ambulance service have not been disrupted.
"There is a significant ransomware attack on the HSE IT systems We have taken the precaution of shutting down all our our IT systems in order to protect them from this attack and to allow us fully assess the situation with our own security partners.
"We apologise for inconvenience caused to patients and to the public and will give further information as it becomes available."
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The HSE said vaccination are going ahead as planned and the National Ambulance Service is operating as per normal with no impact on emergency ambulance call handling and dispatch nationally.
The Minister of Health Stephen Donnelly said: "I have been in regular contact with Paul Reid [HSE Chief Executive] this morning about this cyber attack on the HSE IT systems. We are working to ensure that the systems and the information is protected. COVID-19 testing and vaccinations are continuing as planned today."
He added: "This is having a severe impact on our health and social care services today, but individual services and hospital groups are impacted in different ways. Emergency services continue, as does the National Ambulance Service."
The SAOLTA group said its vaccination centres in Donegal, Sligo, Mayo, Roscommon and Galway are unaffected by the IT system interruption and are operating as normal today.