The Nats spokesperson said: “The issue in our Prestwick centre is now fixed. We are working with airports and airlines to safely lift air traffic regulations as quickly as we can to minimise any further disruption.
“Passengers should still check the status of their flight with their airline. We apologise for the disruption.”
Transport Secretary Heidi Alexander posted on social media that the problems were “deeply frustrating for passengers after the previous issue”.
Passengers have also taken to social media to confirm they are experiencing delays at Glasgow, Prestwick and Edinburgh airports.
Delays are also being reported at Manchester, Newcastle and Belfast airports.
The Manchester Airports Group said there have been delays of up to an hour on some flights at Manchester Airport and there are also delays at East Midlands Airport.
Several arrivals and departures at Belfast City Airport are cancelled, including flights to and from Manchester, Amsterdam, London City and, later on towards lunchtime, Glasgow and Edinburgh.
Dundee and Benbecula airports have also confirmed flights are impacted.
A spokesperson for Edinburgh Airport said: “We are experiencing some delays due to the Nats issue at Prestwick Centre.
“We are monitoring the situation closely and are working with Nats as they work to resolve the issue.”