Close contact alerts on the Covid Tracker app were delayed on some Apple devices.
The HSE says the issue was caused by an authentication token not synchronising correctly within the app.
The health service says the problem is now resolved and was limited to iOS only.
It says it is improving monitoring of the back-end database to identify any similar issues in the future.
Tech journalist Jess Kelly says it is unclear which devices and how many have been affected.
"What I would say to people is don't just ditch the app, it is still worth having on your phone.
"If you are unsure you can go into the settings on your phone, scroll down to 'exposure notifications', and if you go into the 'exposure log' you will be able to see if your phone has been one of the ones that has been impacted.
"But the HSE has said that even if you were, you will still get the notification if you are due one."