The Irish Aviation Authority has reopened Irish airspace following issues with the flight radar system.
A back-up system has been deployed to allow a phased resumption of take-offs and landings at Cork and Shannon.
A knock-on effect to some early morning flights is expected and passengers have been asked to contact their airlines, however Cork Airport has said there will be minimal disruption to flights.
In a statement, the IAA said safety was its main priority and in accordance with normal procedure it had restricted air traffic while the issue was being investigated.
It said it moved to back-up systems as part of planned contingency, and that flight restrictions have been lifted.
The authority said that traffic flows are now in the process of being restored to normal capacity and that flights are now operating again to and from Shannon and Cork.
An investigation into the issue is ongoing and intending passengers have been urged to check with their airlines.
Cork and Shannon airports had earlier said there was a "significant systems failure" with the radar system in the south and west of Ireland, which had resulted in a "zero flow rate" in Irish airspace.
Dublin Airport was not affected by the issue. The airport said its schedule was operating as normal.
The last scheduled departure from Cork tonight, to London Stansted with Ryanair has taken off from the airport, with just one cancellation to London-Heathrow.
The return inbound flight from London-Heathrow was also cancelled as well as an Aer Lingus flight from Birmingham.
At Shannon Airport, a spokesperson said that most flights due in and out of the airport tonight will land at the airport.
A Ryanair flight, FR 3326 from Krakow to Shannon, was due to divert to Dublin but returned to Shannon.
An Aer Lingus flight, EI387 from Heathrow to Shannon which was due to divert to Dublin, has now returned to Shannon.
Another Aer Lingus flight, EI 3638 from Shannon to Birmingham, has been cancelled and passengers accommodated in local hotels overnight.
Additional reporting: Paschal Sheehy, Jennie O'Sullivan and Aisling Kenny
