A school in Cambridgeshire is believed to be among the first in Britain to use facial scanners to register students when they arrive on site.
St Neots Community College is taking part in the research project with Northampton biometric firm Aurora.
The system has been installed in the Post 16 Centre to record attendance.
But David Clouter, of the pressure group Leave Them Kids Alone, said: "It is alarming that this information will be stored on school systems."
The school's deputy principle Scott Preston said it was not aimed at keeping track on truants and students currently use a manual system to sign in and out of college.
With the new system, students walk up to a scanner, type in a pin and are verified within 1.5 seconds.
The scanner takes 15 infra-red photographs of each student before storing the best 10 on a computer alongside their exam number.
The images are not recognisable to the human eye and are used to identify students by pupillary distance and other facial measurements.
Mr Clouter said: "There's no way a school could have the level of security of the passport office. That would cost millions and schools would not have the budget.
"If the data itself is ever compromised, that's it - you can't rewind and get a new face or get new fingerprints."
Paul Coase from Aurora said: "At St Neots it is incredibly secure and it's encrypted. That is pretty standard across local authorities and schools.
"The kind of data that's stored is a grainy infra-red image of a student. The image is stored as an encrypted biometric template. As it's encrypted, it's almost impossible to extract any information from."