Schools are to get the go-ahead to fingerprint pupils as young as five, in new measures to be approved by the Government.
Ministers will issue guidance telling schools they have the right to collect biometric data and install fingerprint scanners.
But the decision has angered opposition MPs who say collecting fingerprints from children will be a gift to identity thieves.
The guidance will say that personal data, including fingerprints and eyeball scans, can be collected from pupils and used to monitor attendance, so long as schools consult parents first and do not share the data with outside bodies.
Schools will be able to place fingerprint scanners at the entrances to classrooms, the school gates and even in cafeterias.
Fingerprint and eyeball scans would make it easy for schools to track children during the day, and tell if they are playing truant, or even what they have eaten for lunch.
MPs fear that school computers are not secure enough to hold biometric data safely and will be unable to erase the information from systems when students have left school.
Civil liberties campaigners accused the Government of wanting to barcode children and questioned whether the data would be kept from other government agencies and the police.
Nearly 900,000 children aged 10 to 17 have their genetic information stored on the police's national DNA database, along with 108 under the age of 10. The guidance, to be approved by ministers this week, will say that schools can benefit from using biometrics at entry points to schools and classrooms as well as to take out library books.
It will warn schools not to give out the sensitive information, telling them it is governed by the same data-protection laws as children's addresses and birthdays. But it is understood that schools will not have to gain written permission from each parent before their child's fingerprints are taken. The guidance, written by Becta, which advises the Government on the use of technology in education, will go out to schools and further education colleges.
The civil rights group Liberty said: "We have some serious concerns that this biometric data is being collected from children simply for administrative convenience. We want to know what happens to the data after the children leave. The police have the right to get into any database, private or public."
About 200 schools are thought to use fingerprint scans already, but most have been waiting for the Government to give the go-ahead. Sarah Teather, the Liberal Democrat education spokesman, said she was concerned that hackers could access sensitive data and steal children's identities. She questioned whether schools would be able to erase the data when children left school.
"We wanted a guarantee that nobody can get hold of this information and an absolute guarantee that the data would be destroyed," she said. "The temptation for schools to reveal this sensitive information to the police will be enormous."
Jim Knight, the schools minister, said he wanted "parents to be fully engaged with every aspect of their children's education - this will be at the heart of our guidance.
"I back every headteacher's right to choose technology to improve their day-to-day running - but it's plain common sense for them to talk to parents about this and all other issues relating to their pupils. Schools need to collect pupil personal information... But we are clear that they have to comply with data protection laws. This means that no outside organisation can access any information."
Further reading: Lords debate, 19 March, Hansard, column 1008