National Air Traffic Services (Nats) said the technical issue causing delays to flights across the UK has stemmed from its control centre in Swanwick, Hampshire.
"Due to a technical problem at Swanwick, we are currently experiencing some difficulty switching from night-time to daytime operation. This may result in some delays, for which we apologise.
"Engineers are working to rectify the problem as soon as possible."
The technical problem affecting the Swanwick air traffic control centre is unlikely to be fixed before 2pm.
Thousands of people have been affected by delays at major airports including Stansted, Heathrow and Gatwick.
The Association of British Travel Agents (Abta) said: "Technicians are working to try to resolve the issue but have advised that this is unlikely to be before 2pm today.
"Delays and flight cancellations at some UK airports are being experienced as a result. Customers due to travel today should liaise with their airline to establish if there are any changes to their flight arrangements."
The association said customers should be prepared for potential delays and advised them to carry essential items such as medication in their hand luggage.
There are delays of up to three hours at Cardiff Airport due to a technical problem affecting flights at airports across the UK. Passengers are being advised to check with their airline before travelling. Further flight information can be found on the Cardiff Airport here.
Cardiff Airport's chief executive Jon Horne has described airline Flybe's decision to drop its Glasgow and Paris routes from the airport as 'unfortunate'.
We are already in discussion with a number of airlines regarding the opportunity to pick up the Glasgow and Paris routes, which currently handle 46,000 and 29,000 passengers respectively per annum. Our focus is on securing an alternative carrier as soon as possible in order to avoid any break in service.
Mr Horne added that Flybe has just added four new destinations from Cardiff Airport, adding: "We will continue to work closely with Flybe and explore with them other route opportunities from Cardiff as their restructuring process continues."
The airline Flybe has announced it is withdrawing its Paris and Glasgow routes from Cardiff Airport from January.
It follows several months of bad press for the airport, which was bought by the Welsh Government earlier this year in a bid to reverse its fortunes.
Paul Simmons, Flybe's Chief Commercial Officer, said: "We have taken a long hard look at all the routes we fly from Cardiff to make sure they are what our customers really want and that they operate at the best possible times for everyone."
The airline said it will still operate its planned schedule to the two destinations to accommodate those travelling for the Six Nations’ matches in February.
It added passengers affected are being contacted and offered, where possible, an alternative Flybe flight or full refund.
Cardiff Airport had to suspend flights for part of this afternoon after an aircraft bust a tyre on landing.
The plane was an Aer Lingus aircraft from Dublin. 37 passengers were safely evacuated and other flights were diverted.
Services are now said to be returning to normal
Airline Flybe is due to announce today four new routes to fly from Cardiff Airport this winter.
The low-cost carrier currently operates flights from Cardiff to 16 destinations, in the UK, Ireland, the Channel Islands and continental Europe.
Details of the new routes will be available later.
Flybe announced it was reviewing its UK operations earlier in the year, with jobs cuts, but said operations at Cardiff would be unaffected.
The airline says today's announcement reflects its "commitment to expanding further its operations to and from the Welsh capital."
The Welsh Government announced bought Cardiff Airport in March, and pledged to turn it around after falling passenger numbers in recent years.
Flight BE1431 from Glasgow was due at 08:30 but is now expected at 11:45.
A spokesman for George Best Belfast City airport said the emergency response was triggered as a "precautionary measure".
Flybe confirmed the incident, saying all passengers would be resuming their journey on a replacement aircraft.
Flybe can confirm that flight BE281 en route to Cardiff this morning returned to George Best Belfast City Airport shortly after take off due to a technical fault. As a precaution and in line with standard procedures the emergency services were alerted. The aircraft landed normally and the 64 passengers and 4 crew disembarked safely and without incident. They will be resuming their journey shortly on a replacement aircraft.
A Cardiff-bound plane has returned to Belfast City airport this morning due to a technical fault.
The Flybe flight landed at around 8am shortly after taking off. All 64 passengers and four crew members disembarked safely.
There was some disruption at the east Belfast facility during the incident. A replacement plane is due to take the passengers on to Cardiff later.