The company has admitted Scots customers using Avios, the BA air miles scheme, have been unable to book their full journey from their home to their holiday destination because of a glitch in the system.
The problem arose because BA releases only a limited number of seats that can be bought using air miles, but they all originated from London airports.
As they are highly sought after, they are usually reserved within hours of being made available.
However, Avios' short haul flights to connect from Scotland to London are released 24 hours later, leaving customers north of the border having to pay cash for the connection on the day the long haul option becomes available or risk waiting to book the full journey using air miles in the hope the flights are still available.
The problem was identified by a Herald reader after he attempted to use his air miles to book a family holiday to Florida next summer, only to find the airline had released the long-haul flights from London to its Avios members a day before short-haul connections from Scotland were available.
Dr Stephen Boyle, 49, a project director for a clinical research firm, has been a frequent flier with BA for about 20 years. Dr Boyle, from Linlithgow, said he had used air miles "very successfully" in the past and had accumulated about 140,000 air miles through his work.
A flight from the UK to the US typically costs around 50,000 air miles per person, regardless of whether the passenger flies direct from London or from Scotland via London.
However, Dr Boyle said he felt dismayed when he logged on to book the holiday only to discover that BA appeared to be "actively discriminating against their Scottish customers".
He said: "London passengers are getting basically 'first dibs', giving them an advantage over their Scottish counterparts.
"BA also does not release domestic air miles flights at the same time as releasing international air miles flights, which again disadvantages Scottish travellers because domestic travel needs to be purchased to ensure the arrival and departure airport is the same."
Dr Boyle said he had checked what it would cost to pay for the domestic connection but was put off when the price came in at about £330.
He also said those connections available to Scottish passengers at the time were only to London City, requiring Scottish customers to make their own way to Heathrow for an international connection - about 27 miles away with no direct link by public transport.
Kevin Thom, of the Scottish Passenger Agents' Association, said: "I am aware of poor availability on many routes if you wish to use Avios points.
"Since the BA-Iberia merger and partnership with American Airlines, where passengers of those airlines can use points accumulated to fly on BA, I have had serious concerns of the impact this would have on the availability of 'Avios' seats for BA passengers.
"As BA allegedly has a superior product and service it would seem natural there would be an element of migration from Iberia and American Airlines passengers to redeem their points on BA."
A spokesman for British Airways said: "Flights are normally available for redemption with Avios 355 days before the departure date.
"However, we have identified an anomaly on our system where seats on some of our long haul flights have been released on the website one day earlier than short haul, leading to the issue experienced by the customer.
"The matter will be fixed as soon as possible, with the discrepancy resolved and the system reverting to releasing both long haul and short haul flights on the same day - 355 days before departure date. We apologise for any confusion this caused."