Schools have been given new guidance on the use of biometric technology in areas such as cashless school meals' systems and borrowing library books.
Fiona Hyslop, the Education Secretary, launched the draft guidance as part of a wider Government drive to help public bodies protect individuals' privacy.
"It is important that school pupils are made aware of the importance of their personal information in relation to any biometric service for school meals or library access," she said.
"When using IT, we need to ensure the mechanisms involved are designed and delivered in such a way that individual privacy is respected. That is why we are developing principles to guide public bodies when designing or developing public services systems, and why consultation on how we manage biometric technology in schools is very important."
A number of biometric systems in Scottish schools are based on fingerprint or palm recognition technology.
In the consultation on the draft guidance, schools are asked to consider whether they actually need such high levels of security as biometric technology, or whether a smartcard might be equally efficient but less intrusive.
Liberal Democrat leader Tavish Scott condemned what he described as "Big Brother tactics" in Scottish classrooms, saying: "There must be better ways to protect security in schools than fingerprinting schoolchildren."
The consultation was welcomed by West of Scotland SNP MSP Gil Paterson, who has backed some parents in East Dunbartonshire, opposed to the use of biometric technology in their schools.
However, Judith Gillespie, development manager of the Scottish Parent Teacher Council, described East Dunbartonshire's system as an example of one that met all the protocols and requirements.
Currently used in two secondary schools for "cashless catering" and being incorporated into six new secondaries, it works by using a fingerprint to create an Alpha Numeric signature which is unique to every individual.
"The fingerprint is then destroyed - it is not stored, it is destroyed. The unique number which has been created cannot then be reinterpreted or `reverse engineered' back into a fingerprint image," said a council spokeswoman. "Pupils and parents are informed about the technology and given the opportunity to opt out. The biometric data is used only for the purpose for which it was collected and is destroyed when a pupil leaves school," she added.