The other airports the air tracker said were worst affected include Gatwick, Manchester and Birmingham.
Flightradar24 found 352 flights to and from Heathrow were delayed, out of its daily average of about 1,300.
Meanwhile, 281 Gatwick flights were delayed out of its 850 total operations average. This was 249 out of 650 for Manchester, and 101 out of 300 for Birmingham.
At time of writing, Nats have 'implemented a fix' and said that their flight system is starting to recover.
In a post on X, Nats, which provides air traffic control services to 15 UK airports, said: "We have implemented a fix and our flight system is starting to recover.
"We are continuing to work closely with our airline and airport customers on recovery.
"We apologise sincerely for the disruption to people's journeys today and they should continue to check with their airline."
Heathrow Airport, the UK's largest airport in west London, confirmed it was among those impacted but said arriving flights were 'currently not affected' in a statement on Tuesday afternoon.
However, in a later update, Heathrow said the issue was 'impacting arriving and departing flights across UK airports'.
Birmingham Airport said the issue was affecting airspace in the south of the UK and was 'impacting a significant number of departing flights across the country'.
Manchester Airport Group, the company that operates Manchester Airport, Stansted Airport in Essex and East Midlands Airport in Leicestershire, said flights from all three had been affected by the issue.
Jersey Airport in the Channel Islands, London City Airport, London Southend, Aberdeen, Glasgow, Southampton and Belfast airports said they were also experiencing some disruption.
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