Flybe has cancelled dozens of flights, blaming “operational issues” including a shortage of pilots, as it told workers it planned to close bases at Cardiff and Doncaster, putting jobs at risk.

Birmingham, Newcastle, Southampton, Belfast City, Aberdeen and Edinburgh were among the airports where a total of 32 flights were cancelled on Wednesday morning, affecting more than 1,000 passengers. Most of the affected flights were to UK destinations.

The airline said: “We have now put in place a number of contingency plans to minimise future disruptions and to manage any repeat of the level of cancellations made today. No cancellations are expected tomorrow.”

Flybe is consulting with employees over plans to close its airbases at Cardiff and Doncaster from 1 October, and to scale back its operations in Exeter and Norwich.

The airline said the changes were part of plans to reduce its aircraft fleet, which means it will stop flying the 118-seat Embraer E195, returning the planes to its lessors. Flybe will continue to fly the 78-seat Bombardier Q400.

Despite closing the bases at Cardiff and Doncaster, it will continue to offer flights to and from both locations on the Q400, with aircraft and crew flying from other bases.

Unite, the UK’s largest union, which represents more than 450 Flybe workers, said 52 cabin crew and 38 pilots were at risk of redundancy at the two sites earmarked for closure. Peter Coulson, the union’s regional officer, said it was seeking to limit the number of job losses and secure assurances about the airline’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,” he said.

“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.”

Brian Strutton, the general secretary of the British Airline Pilots’ Association (Balpa), said Flybe’s decision was disappointing.

“This will come as a shock to all staff. Balpa will be working closely with the airline to ensure pilots’ jobs are protected and that this difficult process is handled as professionally as possible,” he said.

The airline apologised to customers affected by the cancellations and said 95% of flights were operating as normal.

“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,” it said.

“Customers are advised to monitor flybe.com and our social sites for up to date information. Due to the high volume of calls being made to our customer call centre, we would ask customers for their patience and to do any necessary rebookings online if at all possible.”

One customer, Marc Burton, tweeted about the cancellation of his flight from Newcastle to Southampton:

Rory Boland, the travel editor at the consumer group Which?, said: “Thousands of people will understandably be frustrated to have their travel plans thrown into chaos by these last-minute cancellations – and 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.”

In one Twitter exchange, Flybe told a customer that her inability to check in online would “most likely be due to the system change we have just undertaken”.

On Monday, Flybe offered customers a six-hour replacement bus service when a flight on the first day of its new route from Newquay to Heathrow could not take off because of a technical issue.

The airline put itself up for sale in November, a month after a profit warning prompted plans to cut costs and reduce flight numbers. It was subsequently bought by Connect Airways, a consortium led by Virgin Atlantic, in a deal valuing Flybe at only £2.2m.

The latest disruption comes at a difficult time for low-cost airlines. Last week, Iceland’s Wow Air stopped flying after failing to secure emergency funding. The Danish airline Primera Air ceased operating in October, a year after the collapse of Monarch Airlines led to the UK’s biggest peacetime repatriation.