BA is to consider seeking compensation from airports operator BAA after security measures forced it to cancel hundreds of flights from Heathrow.
British Airways' boss has criticised BAA's security search processes
BA boss Willie Walsh attacked BAA's management, saying it had "no adequate plan" to deal with the emergency.
All UK airports have now relaxed the restrictions on hand luggage introduced following Thursday's terror alert.
BA says that since the alert began some 10,000 bags have gone missing and that 5,000 bags still need to be returned.
Airport operator BAA has said searches mean flight delays are likely to continue.
BA has cancelled 700 Heathrow flights since Thursday after requirements to check in hand luggage caused delays.
Analysts have speculated that lost revenues from flight cancellations could cost BA more than £40m, the amount it lost as a result of last summer's strike by baggage handlers.
The carrier has been forced to use trucks to ferry baggage left behind at Heathrow to destinations such as Manchester, Edinburgh and Frankfurt as well as using space in its own cargo aircraft.
BA said: "We fully apologise that customers have not been able to travel with their baggage on certain flights throughout the past five days of unprecedented circumstances at Heathrow.
"This is due to a combination of issues with the BAA's baggage systems which have all contributed to the situation.
"We are working as hard as we can to re-unite bags with customers as soon as possible."
BAA said the easing of restrictions - allowing passengers to take one small item of hand luggage - did not constitute a "return to normal" and passengers should still expect delays.
It admitted there were delays at its security checkpoints but said it believed enough staff were now in place.
BA said the company should have been better prepared and hired extra staff.
"BAA had no plan to keep the airport functioning properly," Mr Walsh said in an article in the Daily Mirror.
The resulting queues resembled a "bad dream at Disneyland", he added.
BA said it would consider what action to take over areas where "it was held back from operating" once its services had returned to normal.
Paul Charles, from Virgin Atlantic, talking about the situation at Heathrow and Gatwick, said the company was running a normal service, adding that it had been a frustrating few days "because we have been forced to cancel a handful of flights we would otherwise be running normally".
Ryanair chief executive Michael O'Leary said BAA were "allowing the terrorists to disrupt the airline transport industry of the UK".
Tim Williamson, marketing director of holiday operators First Choice, said: "It's been five years now since 9/11, and we're actually disappointed that we've got to this point.
"We would have thought that the relevant authorities would have put a contingency plan in place."
The government announced on Monday that the terror threat to the UK had been downgraded from "critical" to "severe", meaning an attack is now considered highly likely but not imminent.
Passengers had initially been banned from taking anything into aircraft cabins except travel documents, baby food and certain medicines, all of which had to be carried in clear plastic bags.
TUESDAY FLIGHT CANCELLATIONS
Heathrow - 47 flights, mostly BA, cancelled
Stansted - 8 Ryanair flights cancelled
Gatwick - 11 domestic BA flights initially cancelled but re-instated at 1230 BST
Airports including Birmingham, Newcastle, Manchester, Edinburgh and Glasgow reported as being mostly back to normal.
But people are still not allowed to take in any liquids apart from baby milk and baby food, and prescription medicines.
A BA spokesman declined to be drawn directly on the issue of compensation.
Meanwhile, police investigating the alleged plot are continuing to search woodland near High Wycombe, while officers have also carried out searches at two internet cafes 18 miles away in Slough.
Twenty-three people are in custody in connection with the suspected plot. Their detentions will be reviewed by a district judge on Wednesday.
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