The UK's largest air traffic control provider has been told to improve its contingency planning after Ryanair claimed staff shortages were delaying flights.
An investigation by the Civil Aviation Authority (CAA) found that Nats, based in Swanwick, Hampshire, had "too few operational staff" following significant cuts, short-term sickness and a reluctance by controllers to do voluntary overtime.
The regulator said Nats needs to boost its resilience by better understanding how shortfalls in resources affect airlines and airports.
Ryanair complained that more than 100,000 of its passengers in London were disrupted due to flights delayed by Nats' staffing shortages in the first half of last year.
In June 2016 some 139 flights to or from the capital were delayed by a total of around 5,000 minutes because of the issue, the Dublin-based carrier said.
Stansted Airport in Essex accused Nats of discriminating against airlines using its airport in favour of those at Heathrow Airport, in west London.
It stated that it was the worst performing airport in the UK for air traffic control-related delays in April 2016.
On the weekend of July 2 and 3 last year controller shortages meant just 10 flights per hour were allowed to land at the airport, down 65% on normal aircraft movements, according to Stansted.
The CAA concluded that Nats had not breached its licence obligations, but did make a series of recommendations.
Richard Moriarty, the CAA's director of consumers and markets, said: "This is the first time that the CAA has used its investigatory powers under the Transport Act 2000 and highlights the potential seriousness of the complaint raised.
"In this instance our investigation has found no compliance breach, however improvements to operational resilience are key to ensuring service delivery levels are maintained in our increasingly busy airspace."
A Nats spokeswoman said: "We welcome the CAA's confirmation today that Nats has fulfilled the requirements of its licence and the Transport Act 2000. This followed a lengthy investigation by the CAA after a complaint was made nearly a year ago.
"The safe air traffic control service that we provide to 2.5 million flights per year is recognised by our customers as one of the best and most resilient anywhere in the world.
"We continually seek to refine our operation particularly in light of the substantial and unforeseen growth of traffic across the South East of the UK since early 2016. Consequently, we are pleased to confirm that we have already taken a number of the actions referred to in the CAA's report."
A Ryanair spokesman said: "Ryanair welcomes the CAA investigation. Delays in UK airspace caused by Nats more than doubled in 2016 compared to the previous year and the CAA's investigation has concluded that the delays were due to a lower resilience in Nats' services.
"The CAA has required Nats to make a number of improvements to its operations, which we hope will prevent delays to Ryanair passengers travelling to or from the UK in the future.
"However, this required level of resilience which Nats failed to provide should not be financed through increased charges to customers, given that Nats is already the second-highest cost air traffic control service provider in the EU, and posted profits of £126 million last year."
A Stansted Airport spokesman said: "We welcome the thorough investigation and the report's recommendation that Nats should identify areas to improve performance and operational resilience at London Stansted.
"We look forward to working in partnership with Nats to improve the way flights and airspace are managed in the future."