The disruption is affecting flights leaving the UK, according to Nats, which provides air traffic control services to 15 UK airports.
Southend Airport said it was affected and apologised to disrupted passengers.
A spokesperson for Southend Airport said: 'We are aware of a Nats technical issue that is currently affecting a number of UK airports, including London Southend.
'We apologise to those disrupted and advise passengers to check with their airline for latest flight information.'
Manchester Airport Group said flights from its three airports—Manchester, Stansted in Essex and East Midlands in Leicestershire—had been affected.
Stansted Airport said the issue was causing disruption to flights at the airport.
A spokesperson for Stansted Airport said: "We are aware of an issue affecting NATS' air traffic control service, which is causing disruption to flights at London Stansted and across the UK.
"Passengers due to travel should check the status of their flight directly with their airline."
Also affected - Stansted Airport (Image: Stansted Airport)
Nats said it was investigating a technical issue affecting some flight departures.
It later said the problem had been identified in its flight processing system.
A spokesperson for Nats said: 'Our engineers are on site and working urgently to resume normal operations as quickly as possible.
'We recognise the ongoing disruption to travel, for which we sincerely apologise.'
Nats said flights were still departing and UK airspace remained open, but warned normal operations would take time to resume.
The spokesperson added: 'Flights are still departing and airspace is open, but recovery will take some time.
"We will provide further updates as soon as possible.'
Passengers have been told to check their flight status directly with their airline before travelling to the airport.
Nats said its engineers were working to restore normal operations.
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