The move has already caused disquiet among some passengers who were handed leaflets warning they would be barred from their flights unless they co-operated.
Anti-ID card campaigners have demanded to know why no public announcement was made and fear compulsory fingerprinting is smoothing the path for the controversial scheme's introduction UK-wide.
The British Airports Authority (BAA), which operates Heathrow, claims the profiling is needed because the new terminal will have a single departure lounge for domestic and international travellers.
The Home Office wants to prevent travellers from bypassing stringent immigration checks by swapping flight tickets once they are through the initial check-in process.
The new scheme works by passengers giving their print and photograph as they pass through X-ray equipment, before their details are verified using the information when they reach their flight's boarding gate.
Dr Gus Hosein, of the London School of Economics who has studied the impact of technology on civil liberties, claimed the government is "softening up" people, particularly the young, by making fingerprinting appear acceptable in the run up to ID cards.
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