The airline says the problems took place on September 20 when at 10:45 BST the Navitaire technology “experienced a technical breakdown”.
An official says online check-in was unavailable for over six hours (restored at 17:00 BST) and bookings could not be taken for a further three hours until 20:00 BST.
Ryanair says it currently has no further details or comment to make about the incident.
The news comes during an unfortunate week for the Accenture-owned Navitaire.
The airline system provider drew an angry response from Asia-Pacific low cost carrier Virgin Blue earlier this week after various services it provides collapsed, stranding thousands of passengers at airports and causing huge disruption to services.
It was the second such incident at Virgin Blue in the space of three months, after a similar outage in June, leading the airline to highlight how Navitaire had supposedly not adhered to existing mission critical service agreements.
Navitaire has not responded to questions about the latest incident with Ryanair. Earlier this week it would not comment or even acknowledge the problems at Virgin Blue.