EasyJet cancelled more than 200 flights over the weekend with disruption expected to last into this week.
The airline blamed the problems on high levels of sickness among employees caused by Covid, with at least 222 trips axed since Friday.
The cancellations left some passengers stranded, amid travel chaos at some of Britain’s biggest airports.
EasyJet said it had made efforts to offset staff shortages by “rostering” additional standby crew on the weekend but was forced to make “additional cancellations for today (Sunday) and tomorrow”.
A total of 62 flights scheduled for Monday have been pulled, the majority of which were announced at short notice on Saturday.
An easyJet spokesperson said: “As a result of the current high rates of Covid infections across Europe, like all businesses easyJet is experiencing higher than usual levels of employee sickness.
“We have taken action to mitigate this through the rostering of additional standby crew this weekend, however, with the current levels of sickness we have also decided to make some cancellations in advance which were focused on consolidating flights where we have multiple frequencies so customers have more options to rebook their travel, often on the same day.
“Unfortunately it has been necessary to make some additional cancellations for today and tomorrow. We are sorry for any inconvenience this may cause to customers on affected flights.
“We have made 62 pre-emptive cancellations for flights to and from the UK for tomorrow which represents a small proportion of tomorrow’s total flying programme which was planned to be more than 1,645 flights.
“We cancelled the majority of these yesterday.”
Some holidaymakers told the PA Media news agency they had been left stranded abroad with no explanation or alternative route home offered by the airline.
It comes as passengers were stuck in long queues at Heathrow Airport on Sunday morning as the Easter holidays began.
The airport attributed the congestion to Covid checks required by destination countries and “high passenger volumes”.
But there were also reports of staff shortages and problems with the e-gate passport checkpoints as travellers took to social media to air their frustrations, with some saying they had waited hours to take off.
Other travellers said several of the automatic e-gates, staffed by Border Force and used to process passengers, were not operating properly.
The Home Office confirmed there had been a “technical issue” with the checkpoints which has since been resolved, and said the problem had not caused queues to exceed the “standard length” at Heathrow.
But a Heathrow spokesperson said: “Due to high passenger volumes and the Covid documentation checks still required by many end destinations, Terminal 2 departures has experienced some congestion today.
“Our teams are supporting our airline partners to get passengers away on their journeys as quickly as possible and we apologise for any inconvenience this has caused.”
Manchester Airport has experienced similar problems in recent weeks as it has struggled to cope with delays due to increased traveller numbers amid staff shortages.
Some travellers landing also voiced complaints about extensive waits in the baggage reclaim halls.
A spokesman for Manchester Airport said passengers were being advised that “security queues may be longer than usual” and urged to arrive early for their flight.
“We apologise to passengers whose experience at Manchester Airport has fallen short of the standards they expected.
“As we recover from the impact of the coronavirus pandemic, our whole industry is facing staff shortages and recruitment challenges.”
They added: “We are aware similar challenges are being faced by airlines and third parties, such as baggage handling agents, operating on our site.”
Like this story? Why not sign up to get the latest South West business news straight to your inbox.
