Peers have criticised the "intrusive" and increasingly common practice of taking schoolchildren's fingerprints.
Schools are being urged to seek permission before taking fingerprints
Junior education minister Lord Adonis defended some schools' use of biometric data for the attendance register, and access to meals and libraries.
He said fingerprints were destroyed once pupils left the school, and were only taken with parents' consent.
But Lib Dem, Tory and crossbench peers criticised the practice as intrusive, alarming and "completely astonishing".
For the Lib Dems, Baroness Walmsley said: "The practice of fingerprinting in schools has been banned in China as being too intrusive and an infringement of children's rights. Yet here it is widespread."
She said one head teacher had "tricked" three-year-olds into giving their prints "by playing a spy game".
And, she said, with the dangers of identity fraud, the practice should be banned unless parents specifically signed up to the system.
Crossbencher Baroness Howe said: "Most people would be somewhat alarmed by the idea of having fingerprints taken and would have connected it with criminal offences."
A Tory peer, Baroness Carnegy, asked Lord Adonis: "Are you not concerned that the impression children are going to get of what it is to live in a free country and what it is to be British if, in order to get the right school meals, they can have fingerprints taken? It seems to me completely astonishing."
The Department for Education and Skills (DfeS) says it does not have figures for how many schools are already using biometric data.
But a web poll by lobby group Leave Them Kids Alone estimated that 3,500 schools had bought equipment from two DfES-approved suppliers.
After pressure from campaigners, privacy watchdog the Information Commissioner is to urge schools to seek parents' permission before taking children's fingerprints.
Some primary schools have stored children's thumb prints for computerised class registers and libraries without parental consent.
Lord Adonis told the House of Lords on Monday that under the Data Protection Act 1998, children or their parents must be given "fair processing" notices about the data and its proposed use.
He said biometric systems could improve the take-up of free school meals, as there was no "stigma" attached and many schools were using the systems "without any contention whatever".
Lady Walmsley accused him of "complacency" and said children were being fingerprinted without permission, and were being victimised if they did not comply and threatened with exclusion.
Lord Adonis replied: "I think there is a certain amount of scaremongering in your question, which I regrettably don't accept on the basis of the information that has been made available to my department."