Both Glasgow and Edinburgh said flights were back to schedule by 19:00.
A technical issue had caused delays to flights through all of Scotland's main airports.
Edinburgh, Glasgow, Aberdeen and Prestwick airports were affected by the incident at the Scottish Air Traffic Control centre at Prestwick.
Air traffic controllers Nats said there had been interference with some radio frequencies used to talk to aircraft.
The organisation has apologised to passengers and said it was also doing everything it could to safeguard the evening rush hour.
Nats said the faulty piece of equipment had now been removed from service.
All flights at Edinburgh Airport were delayed while three Glasgow Airport flights were cancelled  - one to Gatwick and two to Amsterdam -  and delays were expected throughout the day.
There were also a small number of delays on southbound flights from Aberdeen Airport.
Nats spokesman Paul Haskins told BBC Radio's Good Morning Scotland programme: "We've had a technical problem overnight with interference with some of our radio frequencies which we use to speak to aircraft.
"It only affects some parts of Scottish airspace and flights from and to some Scottish airports but there may be delays as a result this morning.
"We have identified the cause and isolated the problem and the situation is now improving."
Transport minister Derek Mackay said: "There was a technical issue that has been rectified and addressed, however there are knock-on consequences to the airlines.
"People should check with their airlines and the airports to ensure that their flights are running."

The former England Under-19 international made four appearances last season as the Belles were promoted from Women's Super League Two.
"I have tried so hard to get back but my legs just won't go," she said in a message posted on Twitter.
"Unfortunately, this disease cannot be beaten and has taken my dream."
Belles manager Glen Harris said: "It is sad that a young player, with the talent Ash has, has had to stop playing at the top level.
"Ash has been a pleasure to work with, always turning up and training with a smile on her face... even if it's not always in the right kit!"
Mills added: "My three years with the club have been absolutely fantastic.
"I have enjoyed every minute of my time here. I feel very honoured to have represented this great historic and successful club."
Mills said she plans to cheer on the Belles from the stands.
Doncaster start the new Women's Super League One season at home to reigning champions Chelsea on 24 March.
Around 100,000 people in the United Kingdom have multiple sclerosis or MS, according to the Multiple Sclerosis Society.
It is normally diagnosed in people between the ages of 20 and 40.
Symptoms might include fatigue, vision problems and difficulties with walking, but MS is different for everyone.
In MS, the protective layer surrounding nerve fibres in the brain and spinal cord - known as myelin - becomes damaged. The immune system mistakenly attacks the myelin, causing scarring or sclerosis.
The damaged myelin disrupts the nerve signals - rather like the short circuit caused by a frayed electrical cable.
If the process of inflammation and scarring is not treated, then eventually the condition can cause permanent neurodegeneration.
Michelle Mitchell, chief executive of the MS Society, said: "MS is an unpredictable and challenging condition to live with and diagnosis can be upsetting and scary. The MS Society is here to help anyone affected by MS."
MS Society helpline: 0808 800 8000.
Scotland's busiest airports have returned to normal after a day of disruption caused by an air traffic control failure.
[NEXT_CONCEPT]
Doncaster Rovers Belles midfielder Ashleigh Mills has ended her playing career at the age of 20 after being diagnosed with multiple sclerosis.