The HSE has placed a temporary ban on external access to its network over fears that its systems could be targeted in a cyber attack.
The health authorities convened a special meeting last night following a global spate of ransomware cyber attacks affecting at least seven countries.
The attacks, which see a virus encrypt a computer's files and demand payment in bitcoin to decode them, began with an assault on NHS hospitals across Britain, using malware called Wanna Decryptor.
NHS hospitals across the North, East and West Midlands, and London were reporting IT failures, in some cases meaning there was no way of operating phones or computers.
It has now emerged that the HSE has taken "protective measures" to remove external access to its IT systems, in what it is treating as a "major incident".
The HSE has also said that it is monitoring the situation and is liaising with both NHS England and NHS Scotland to gather intelligence and offer any necessary assistance.
In a statement after last night's meeting, the HSE said: "It was decided that, as a protective measure, the HSE's Office of the Chief Information Officer would remove all external access to the HSE's network to protect the integrity of clinical IT systems throughout our health system."
The ransomware cyber attacks affecting companies and government organisations in at least seven countries began yesterday morning.
Pictures posted on social media showed screens of NHS computers with images demanding payment of $300 (€274) worth of the online currency Bitcoin, threatening to delete files within seven days.
At some hospitals, patients were being told not to come to A&E with all non-urgent operations cancelled.
Russia, Ukraine, and Taiwan were the worst hit by the attacks. Attacks were also detected in Spain, the Philippines, and Kazakhstan, Turkey, Vietnam, Germany, Indonesia, and Japan.
Twitter users also reported similar attacks in Pakistan and Italy.