Schools in England will be banned from collecting pupils' biometric data without consent, the Department for Education (DfE) said.
From September next year schools will be forced to obtain parental permission before taking fingerprints.
The ban will also cover the use of data for iris and retina scanning, and face recognition.
According to the DfE approximately 30% of secondary schools and 5% of primary schools use fingerprinting or face-scanning systems for a number of reasons, including recording attendance, allowing pupils to check out library books, pay for lunch or access certain school buildings.
Schools Minister David Laws said: "Many parents do not want schools and colleges collecting personal information from their children without permission.
"These tough new rules will mean that, for the first time, parents will have the power to stop schools from using their child's biometric data - like fingerprinting or facial recognition - unless they agree first."
The new provisions in the Protection of Freedoms Act 2012 will apply to all England's schools, sixth form colleges and further education institutions where education is provided to children.
Schools will have to make sure any data collected from pupils is treated with the appropriate care, and make alternative arrangements for children who refuse to have their data taken.