Some see them as threats to civil liberties, but virtually every secondary school in the country uses some kind of biometric identification system.
Now the Association of School and College Leaders (ASCL) is warning, however, that an "unnecessary" new law means the technology - which digitally recognises pupils' fingerprints, irises or other parts of their bodies - will cost schools millions of extra pounds.
The problem is a clause in the Protection of Freedoms Bill currently going through Parliament, which will force all schools using the systems to gain retrospective permission from both parents of every pupil.
This is excessive to say the least, according to the heads. They say that, at a very conservative estimate, it will cost the sector nearly #163;2 million as staff contact and chase every single parent.
But BioStore, a firm supplying the systems - used for everything from building entry to library loans and school-dinner payments - has gone much further, claiming that getting parental permission will add #163;8 million to schools' costs.
"It is an administrative job that is going to take a lot of time per child in even the most effective schools," said ASCL deputy general secretary Malcolm Trobe.
Heads' lobbying has so far failed to persuade politicians to amend the bill. During its second reading in the House of Lords last week, Conservative Home Office minister Lord Henley said schools needed "to have proper regard for the sensitive nature of personal biometric information, so it is right that parents should be asked to make an informed decision".
The legislation follows concerns that biometric systems are being used to turn schools into "authoritarian fortresses". Some civil-liberties campaigners have claimed that they will jeopardise "the privacy of students for the rest of their lives" and create the possibility of a "database by the back door".
But the ASCL argues that the Government and campaigners have misunderstood the nature of the school systems. "The use of biometric systems for access, library and catering purposes in schools and colleges is being confused with the use of biological material and biometric data in the criminal and terrorism contexts," a briefing from the association said.
"The biometric systems in use in education do not precisely identify individuals in the general population in the way that police fingerprinting may do, but merely distinguish between different pupils well enough to charge the correct ones for their lunch. The information would not therefore be sufficient for investigative, forensic or evidential purposes."
Schools believe that biometric systems are efficient and avoid the stigma that can be attached to receipt of free school meals, the possibility of fraud through lost or stolen cards and pupils being bullied for dinner money.
Mr Trobe said he doubted that schools would abandon the systems because of the new law, which will also give pupils a right to refuse to participate and compel the school to find alternatives in such cases.
But it would mean extra expense and bureaucracy. Mr Trobe was backed by Conservative peer Lord Lucas, who last week told the Lords that the clause was "a daffy overreaction". "Biometric systems are very widely used in schools," he said. "They have great benefits.
"We are dealing here not with something that is available nationally, but with a closed system, a community that is using this data within itself."
Lord Lucas said he hoped to get the bill amended, because there would be increased bullying "particularly where free school meals are concerned" if schools were not able to use biometric systems consistently.
But as the opportunities to change the legislation run out, heads' leaders are working out how they can lobby for regulations that will give schools as much latitude as possible when chasing parental permission.
School leaders' experiences of biometric systems, collected by the ASCL:
"We have found our biometric system to be an absolute godsend for all of the reasons others have outlined, and removing it would take us back to chaos. There is no issue whatsoever with either parents or students accepting it."
"Remember, it is not fingerprinting. It is finger recognition. A very different concept."
"An opt-out is offered. Two have declined in five years and chosen cards. That's two out of approximately 2,500 pupils who have passed through."
"The number of students taking free school meals has gone up dramatically. They are now enjoying a hot, well-cooked meal which is nutritional and helps learning."
"It would be madness to remove the ability of schools to use such good, technologically advanced and safe systems."