Flybe has cancelled dozens of flights and announced it will stop flying jets from four airports.
The regional airline said a shortage of pilots was one of a "combination of factors" causing disruption on Wednesday, but insisted the cancellations were "not linked" to a decision to reduce its aircraft fleet.
Passengers travelling to and from Aberdeen, Belfast, Birmingham, Cardiff, London Southend and Southampton were among those whose travel plans were thrown into disarray.
The airline operates flights between Newcastle and Aberdeen, Cardiff, Exeter, Newquay, Paris and Southampton.
It also runs flights from Durham Tees Valley to Aberdeen, Humberside and Jersey.
A flight from Newcastle to Southampton was among those cancelled today, though no other issues were listed for North East airports.
The Exeter-based carrier said in a statement: "Flybe sincerely apologises to all our customers and partners affected by the current flight cancellations.
"Whilst 95% of Flybe flights are operating as per normal, we do recognise the impact of today's cancellations.
"We are doing our best to mitigate the impact of the current situation that has arisen due to a combination of factors including seasonality, pilots' end of leave year, Easter holidays, base restructuring and the shortage of pilots across the industry that Flybe has highlighted over recent months."
Flybe also announced changes to its bases from October, as it returns all its 118-seater Embraer 195 jet aircraft to their owners. It will continue flying 78-seater Bombardier Q400 turboprops.
The end of jet flights means its bases at Cardiff and Doncaster Sheffield will be closed, and its operations at Exeter and Norwich will be reduced.
Unite union regional officer Peter Coulson said: "Unite is seeking to minimise the potential job losses and secure assurances about Flybe's long-term future.
"Our members are justifiably concerned about their jobs and future employment, as a result of the company cancelling a number of flights for 'operational reasons' and having launched a redundancy programme.
"It is essential that Flybe is fully transparent with its workforce about the exact situation facing the company. The current uncertainty is incredibly unsettling and is in danger of severely damaging morale at the company."
Flybe chief executive Christine Ourmieres-Widener said: "Our fleet reduction has always been core to improving our profitability.
"We are committed to assisting all our affected employees across the impacted Flybe bases.
"We remain fully committed to Exeter, Cardiff and Doncaster airports and will continue to offer a comprehensive choice of regional and European destinations operated by our 78-seat Bombardier Q400 aircraft."
Editor of Which? Travel magazine, Rory Boland, said: "Thousands of people will understandably be frustrated to have their travel plans thrown into chaos by these last-minute cancellations.
"The lack of clear information provided by Flybe was completely unacceptable.
"All passengers affected by these cancellations are entitled to a full refund or to be rerouted on to another flight to their intended destination - and to over £200 compensation under European air travel rules."
Flybe flies 8.5 million passengers each year to 170 European destinations.
In February the airline was bought by a consortium led by Virgin Atlantic following poor financial results.
Connect Airways, which consists of Virgin Atlantic, Stobart Group and Cyrus Capital, paid £2.8 million for Flybe's assets and operations.