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The £1.2bn e-Borders security system flagged more than 48,000 travellers for intrusive background checks last year, it has emerged.

Those automatically matched against intelligence watch lists are subjected to scrutiny of their criminal and financial records, as well as checks of their known associates.

The system currently covers only air travel, but is scheduled to screen all journeys in and out of the UK in 2014. The previous government approved e-Borders in 2004 amid controversy over wildly inaccurate immigration figures.

According to the Mail on Sunday, the system is being used to track sex offenders and football hooligans. Last year's 48,682 security alerts led to 2,000 arrests, it was reported. Some 1,000 people were denied entry to the UK as a result of e-Borders checks and 14,000 intelligence reports were created for future use.

Airlines supply the National Border Targeting Centre in Manchester - the centre of the e-Borders network - with information on passengers' travelling companions, their meal choices and how they paid for their ticket.

Hundreds of low-paid "match analysts" receive reports from the profiling system when this information, combined with previous travel histories and watch lists, raises a security alert. The reports are checked and passed on to police and intelligence agencies as deemed appropriate.

The MoS reported an internal Home Office document cited an example of when the profiling algorithms fail. One "potential suspect" was in fact a spinal injury patient travelling home with his nurse.

Separately this weekend, the Sunday Times reported that new government sources said the ongoing e-Borders implementation "is running even later and more over-budget than Labour ministers had admitted". A Home Office spokesman denied the claims today. ®

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