Schools are being given official guidelines to clarify how they can use and store pupils' biometric information, such as fingerprints.
Biometric systems are used in school for registration and payment
There are schools which use biometric systems for registration, meal payments and for taking books from libraries.
This has prompted privacy concerns and uncertainty about the legal status of holding fingerprints from children.
The guidance says schools must destroy data when pupils leave school and not share any such biometric information.
"Schools are well used to handling sensitive information like attendance registers, behaviour records and home addresses. But we are absolutely clear that they have to comply with data protection laws," says Schools Minister Jim Knight.
"That means that this data can only be used for its stated purpose; cannot be shared with third parties beyond this stated purpose; and it must be destroyed when a pupil leaves their school."
But the Conservatives have criticised the guidelines as "weak" and failing to provide unambiguous guidance for schools.
"This is long awaited but very disappointing guidance," says Shadow Schools Minister Nick Gibb.
"It is very weak as it neither requires schools to seek parental consent nor recognises the serious issues at stake with schools fingerprinting children simply for administrative convenience."
The advice from the government's school technology agency, Becta, addresses the kind of school administration systems which use a physical identification system, such as fingerprints.
There are schools which use fingerprints to identify individuals arriving at school, in a tactic to reduce truancy. Pupils would touch a fingerprint reader to show they were in school or in an individual lesson.
But there have been concerns about how such personal biometric data is stored or who else might have access to such information.
And there have also been disputes about the rules governing the collection and use of such data from young people.
In the House of Lords, Baroness Walmsley said that 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".
The guidance from Becta says that schools should not store biometric data after pupils have left - and that any information can only be used for the specific purpose for which it was given.
So if children are asked to give fingerprints for use in a library system, the biometric information can only be used in that specific context.
When children leave school, or the original purpose no longer applies, schools will be expected to destroy this personal information.
Schools are also barred from handing over such information to any other organisation.
There is also a requirement for schools to have sufficient security to protect this data.
Schools are being urged to get parents involved in discussions about the use of biometric systems, so that any privacy concerns or other doubts can be addressed.
The schools minister says that many schools have seen the benefit of biometric systems, in simplifying administration, but that they need to keep parents aware of how information is being stored.
"I have seen at first hand how well these systems work. They can speed up lunch queues, remove the need for children to carry money and take away the stigma of singling out those on free school meals," says Mr Knight.
"Moreover, they can enable schools to register pupils more easily as they move from class to class."