Pilots are refusing to take part in the upcoming ID card trials for airside workers.
18-month trials are due to start this autumn at Manchester and London City Airports, but the union, which represents 10,000 commercial pilots, says its members will not take part.
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The British Airline Pilots Association (Balpa) says its members are refusing to be guinea pigs for the scheme.
Balpa says the ID cards will not make security arrangements easier for pilots, who already have to hold a different pass for every UK airport.
A recent poll by the union found 40% of pilots felt "less able to operate the aircraft" as a result of stress caused by slow security processes.
The Home Office has said the trials will be voluntary, but Balpa says it is not possible to get the security passes pilots need without having an ID card.
General secretary Jim McAuslan said, "Our members believed the government promise that the national ID card would be voluntary, but they now know it is anything but. Our members must have an airside pass to operate aircraft and now discover that to get that pass they must have a national ID card."
McAuslan added pilots are concerned about what will happen to the data they are being asked to provide the government with. "Like every other citizen, they ask themselves what will happen to the data they are coerced into providing; whether it will it be safe, whose hands might it fall into, and what might they do with the data? Yes, there have been lots of reassuring noises, but frankly we don't believe them. Our members increasingly have a sense that a line is being crossed in the relationship between state and citizen; a sense that Big Brother knows best."