An investigation has found there was a delay in 21 infants receiving medical care last year - after their referrals were sent by fax.
The review for 2016 was carried out by the Ombudsman for Children across some 2,000 hospitals.
Fax and post are used for referrals throughout the country, with just 20% of referrals taking place electronically.
Richard Corbridge, chief information officer at the HSE outlined why the transfer to digital is taking so long.
"It's resources - IT in all industries is an expensive thing to do, it's a time-consuming thing to do," he said.
"Cork alone had 9,000 hours of training before it went live in December of last year.
"You're taking people from paper and pen to using tablet PCs, so we've got to do each hospital carefully.
"Later this year, two more maternity hospitals will go live. The ability to have cancer care through an electronic cancer record will start this year."