The Irish Aviation Authority (IAA) has expressed its "regret" at any inconvenience caused, after a technical issue affected Shannon and Cork airports on Tuesday night.
It comes as the aviation body is continuing to investigate the problem at the Shannon Air Traffic Control radar system, which closed large parts of Irish airspace.
Flights in and out of Cork and Shannon Airport were suspended for a time - with no planes allowed to enter the impacted airspace.
Dublin and Belfast airports were unaffected.
In a statement earlier, the IAA said the flight restrictions were introduced in accordance with normal procedure, while the issue was being investigated.
The authority said services to and from Shannon and Cork are operating normally on its Shannon back-up system.
— IAA (@IAApress) October 3, 2018
While the Department of Transport said: "The minister was advised late yesterday evening of a systems failure which affected air traffic control services run out of the Irish Aviation Authority’s Ballycasey, Shannon facility.
"This resulted in some delays to flights into and out of Cork and Shannon airport for a period last night.
"The IAA has advised the minister that it transferred successfully to a back-up system last night and that air traffic control services are currently operating as normal, without delays.
"The company has expressed its regret at any inconvenience caused but, rightly, it put the safety of the aircraft and its passengers first in all of the decisions that were taken.
"The IAA is now focusing on investigating the cause of the failure in its frontline system and working to bring it back up on-line as quickly as possible."
The IAA said flight schedules are returning to normal.
However, passengers are being urged to check with their airline as some delays are expected.
The system used by the IAA is called COOPANS ATM.
It was developed and is operated under a joint partnership with other EU member states: Austria, Denmark, Croatia, Portugal and Sweden.
There are no reported technical difficulties in the other partner states.
Additional reporting: Jack Quann
