The volcanic ash, which followed an volcanic eruption in Iceland, was expected to have cleared UK airspace by 1am today.
Dozens of flights to and from Scotland and Newcastle were cancelled but Transport Secretary Philip Hammond held out hope that the worst was over for air passengers.
However Nats advised passengers to continue checking airline updates before travelling.
More than 250 flights were cancelled across Europe yesterday after plumes of ash spewed across the continent. Scottish airports were badly affected, with hundreds of passengers forced to wait for hours only to discover their flights had been cancelled last night.
Newcastle, Carlisle and Durham Tyne Tees Airports also faced disruption, although skies further south – including those over Yorkshire – remained clear. British Airways, EasyJet, Ryanair, Aer Lingus, Flybe and KLM were among carriers cancelling flights.
Ryanair had earlier railed against official announcements that the ash cloud above Scotland was of “high density”, sending up a test flight over Scotland which it claimed proved there was “no volcanic cloud” over the country.
Outspoken chief executive Michael O’Leary had said the CAA should “take their finger out of their incompetent bureaucratic backsides and allow the aircraft back into the skies.”
He claimed the so-called “red zone” of high-density volcanic ash was “non-existent, mythical and a misguided invention”.
However, Ryanair was the first airline to cancel all scheduled flights to and from Scotland for the remainder of the day.
The Barcelona football team due to play the Champions League final against Manchester United at Wembley on Saturday flew into England early last night to avoid any chance of being stranded in Spain.