British Airways has criticised Heathrow owner BAA for allowing George Bush to fly into the UK's biggest airport, forcing the cancellation of at least 69 flights and disrupting the travel plans of 40,000 passengers.

Willie Walsh, BA chief executive, said he was angry that the presidential entourage, which included two Boeing 747 jets and four helicopters, caused chaos 10 days ago as runways were closed and planes grounded. "The decision to allow President Bush and his fleet of aircraft to fly into Heathrow rather than a military base was one all of Heathrow's users could have done without," he said. "I am also angry that this was allowed."

Walsh said the disruption began two days before the president's visit on June 15 and lasted for the two days that his party stayed in the UK. Heathrow was reduced to one working runway for 30 minutes on June 15 and 16, after its other runway was closed temporarily for the arrival and departure of Air Force One.

According to BA, there was a ban on departing flights on two separate occasions as the president arrived, leading to knock-on delays that lasted six hours. A rehearsal on the preceding Friday, when two helicopters landed at Heathrow, caused similar delays, BA said. Walsh blamed the disruption on the size of the entourage and US security requirements.

BA, Heathrow's biggest customer, said it had cancelled 53 short-haul flights while more than 260 flights were delayed by more than 30 minutes, affecting 38,000 passengers.

BAA admitted a further 16 flights from other airlines were cancelled for the duration of the president's visit. But it defended its decision to allow Air Force One to land, saying Heathrow was the best port of entry for the party, given an itinerary that included a dinner at Windsor Castle, while the airport offers a high level of security, acquired through many years of handling VIPs.

Writing to BA staff in the airline's in-house newspaper, Walsh said the carrier was well used to disruption at the airport, but what was different on this occasion was that the delays were "completely unnecessary".

BA has endured one of its worst ever years at Heathrow, after the disastrous opening of Terminal 5 forced the cancellation of more than 500 flights and heaped bad publicity on the airline. However, the £4.3bn building has been working smoothly since then.

Ruth Kelly, the transport secretary, is expected to reiterate calls for a third runway at Heathrow tomorrow when a report is published on the causes of delays and cancellations. BA and BAA claim disruption is common because its two runways operate at capacity, leaving no room for recovery if freak weather, security scares or a presidential visit upset flight schedules. Four out of 10 Heathrow flights are late, with an average delay of 25 minutes.

A BAA spokesman said: "BAA, the airlines and other business partners at Heathrow did everything in their power to minimise disruption at the airport during George Bush's presidential visit. Despite our best efforts, some disruption did occur, for which we apologise to passengers affected."