The commissioner is also concerned that parents are not allowed legal redress after one man was told he could not challenge the compulsory fingerprinting, without his permission, of his daughter for a "unique pupil number".
In many schools, when using the canteen or library, children, as young as four, place their thumbs on a scanner and lunch money is deducted from their account or they are registered as borrowing a book.
Research carried out by Dr Emmeline Taylor, at Salford University, found earlier this year that 3,500 schools in the UK – one in seven – are using fingerprint technology.
EU data protection rules, Brussels legislation that overrides British law, requires that the gathering of information such as biometric fingerprints, must be "proportionate" and must allow judicial challenges.
"We should be obliged if you could provide us with additional information both regarding the processing of the biometric data of minors in schools, with particular reference to the proportionality and necessity in the light of the legitimate aims sought to be achieved, and the issue concerning the availability of judicial redress," said the letter