As voters express concern about surveillance technology, is it becoming second nature to the Facebook generation – used to publishing intimate details of their private lives on the worldwide web – who, in later life, may be less vociferous in their opposition to such schemes?

An increasing number of today's schoolchildren are forgoing the humiliating daily name call of registration, and are instead having to "fingerswipe" in and out of class, or to give it its proper name: biometric registration. According to campaign group LeaveThemKidsAlone, schools have fingerprinted more than two million children this way, sometimes even without their parents' consent. A statement on its website claims: "It's part of an enormous softening-up exercise, targeting society's most impressionable, so they'll accept cradle-to-grave state snooping and control."

Hard-pressed schools and local councils with tight budgets are being enticed by a new generation of software that promises to cut administration costs and time. In the last 18 months, several Guardian readers have written into the paper expressing concern at this new technology being trialled on their children. Everything from "cashless catering schemes" to "kiddyprints" instead of library cards is being introduced by stealth into the nation's schools, it is claimed.

The software companies that are jostling for a stake in this lucrative market, such as VeriCool and CRB solutions, boast several testimonials on their websites, arguing that this technology not only minimises lunchtime queues and paperwork, but also tackles more serious problems such as truancy and bullying (a cashless system negates the need to be biffed for your lunch money). They even claim that their systems promote healthy eating, as pupils accrue points for eschewing sugary snacks.

Furthermore, CRB solutions is quick to reassure pupils and staff that "this wasn't the same sort of fingerprinting that the police did … in fact, parts of the 'fingerprint' are converted (using a mathematical algorithm) into digital data which can then be used for future recognition."

However, the police and security services do use coded algorithms when taking the fingerprints of a suspect, as well as taking inky fingerprints that are kept on paper file. And it is this data that they use to match fingerprints at the scene of a major crime. The implications are vast – the nation's schools aren't exactly the safest place for the storage of this sensitive data – and anyone with access to the system and a mobile SIM card can download the information from a computer, increasing the chances of identity theft. Unless the computer system is professionally purged, before this data has a chance to be leaked, it can remain in cyberspace for eternity to be retained for all sorts of dubious purposes.

It's odd that this drive towards fingerprinting children coincides with the government's keenness to expand the national DNA database – we already have one of the largest in the world – with more than four million people on file, including nearly 1.1 million children.

Odd too that VeriCool is reported to be part of Anteon, an American company that is responsible for the training of interrogators at Guantánamo and Abu Gharib.

It seems that in the blink of an eyelid (or iris scan), our children are losing the civil liberties and freedoms we are fighting so hard to preserve.