British Airways has begun cancelling flights ahead of a second strike by pilots later this month.

The airline confirmed cancellations with thousands of passengers around 27 September, when pilots in the Balpa union are due to walk out for another 24 hours, in a dispute over pay and conditions.

BA cancelled about 1,700 flights during the first strike on Monday and Tuesday, with some disruption continuing into Wednesday. The cost to the airline was estimated to be about £40m a day.

Pilots have demanded a profit-share scheme and rejected a three-year pay deal worth 11.9%, claiming they have been let down by the airline after supporting it through several lean years.

The travel plans of tens of thousands of passengers are likely to be affected, although the airline had warned customers of likely cancellations when the first wave of strike dates were announced on 23 August. It also removed flights from sale. BA would on a normal day carry an average of 145,000 passengers.

In a statement, British Airways said: “It is now a month since we shook hands on a pay deal. We urge [Balpa] to call off their strike and return to negotiations.

“To give our customers as much certainty as possible, we are now contacting all those affected to offer them a full refund or a rebook on an alternative date, destination or airline. We are very sorry that Balpa’s actions will affect thousands more travel plans.”

Extra staff have been drafted in to work on BA’s phone lines after it drew criticism that it failed to respond to customer queries when the first cancellations were announced. The airline said its customer relations teams have now dealt with almost half a million telephone calls since the strike dates were set by Balpa.

Balpa had said it would hold talks to avert further strikes but that it wanted “meaningful negotiations”, adding that BA had to improve its offer.

The union accused the airline of being “irresponsible and inconsiderate” to customers by cancelling flights now rather than holding talks. BA would be liable for additional payouts to passengers, covering costs such as hotels, if it cancelled with less than 14 days’ notice, under EU261 flight compensation rules.

A Balpa spokeswoman said: “Balpa set a gap between the first and second periods of strike action to give BA time to work with us to settle this dispute with their pilots. We had today been exchanging new ideas to do that via [the arbitration service] Acas and so it irresponsible and inconsiderate to its customers that BA has pulled out and decided to start cancelling flights now, just to save money on compensation. BA did not respond to our latest proposals before cancelling these flights.

“Passengers who will be affected by these cancellations should know that we have given BA multiple opportunities to work with us so we could call off this action.”

The consumer group Which? said customers with bookings should beware of being “fobbed off” by British Airways. Adam French, a consumer rights expert at Which? said: “BA must now proactively inform those affected by any fresh cancellations of their rights to be rerouted on the next available flight, even if this is with a rival airline.

“Unless a refund is vital to you, don’t be fobbed off by this option. A refund means your travel plans would no longer be the responsibility of the airline and you would not be entitled to any reasonable out-of-pocket expenses incurred because of the disruption.”

The union has a mandate for further industrial action until January.