BA later apologised after admitting that some passengers were mistakenly told that their flights were cancelled on non-strike days. BA admitted its customer service phone lines were busy but said its website was working fine.
"We are doing absolutely everything we can to prevent this unfair action from taking place and ruining our customers' travel plans," said BA.
"Airlines have a very complex operation and during times of widespread disruption, there can be knock-on effect on to flights on other days," it added.
Last month, members of Balpa voted 9-1 in favour of strike action, on a 90 per cent turnout. BA subsequently failed in an attempt to block mass walkouts through a court injunction.
Balpa said the decision to go on strike was a "last resort" and had been taken with "enormous frustration at the way business is now being run".
It added that "it is clear following discussions with members over the past few days that BA's most recent offer will not gain the support of anywhere near a majority of its pilots".
The airline said it had made a "very fair offer" and it was "completely unacceptable that Balpa is destroying the travel plans of tens of thousands" of customers.
BA said its pay offer of 11.5 per cent over three years was fair and highlighted that the Unite and GMB trade unions, which represent nearly 90 per cent of all BA workers, had recommended the same pay offer to their members.
The airline said it was making changes to its schedule but added that it was likely that many of its customers would not be able to travel. It said it would offer refunds and re-bookings for passengers booked on cancelled flights.
BA said it was exploring options to supplement its fleet with aircraft and crew from other airlines, a practice known as wet-leasing. It was also working with partner airlines to schedule larger aircraft to take more customers.
The strike action comes amid separate walkouts by Ryanair's British pilots, which end on Friday. The Irish low-cost carrier on Wednesday lost a High Court bid to block a two-day strike by its British pilots, represented by Balpa, but the carrier faced minimal disruption.
BA said it is offering all customers booked to travel on affected flights options to rebook to a different date or take a full refund.
Written by: Tanya Powley
© Financial Times 2019