Youngsters attending high schools in East Dunbartonshire have been asked to supply their fingerprint in order to gain access to a fund set up by their parents or guardians.
It will allow them to purchase snacks and meals throughout the school day.
But worried parents have hit out at the payment process claiming there are no guarantees the data will be kept secure.
A letter sent out to parents confirms East Dunbartonshire Council will do "everything it can" to minimise data breach risks.
However, it also stated no computer system can be guaranteed as "100 per cent secure" - prompted outrage from parents.
One dad, who asked not to be named, said: "I'm really unhappy at the thought of my 11-year-old daughter's fingerprint being held on a council IT database.
"Massive blue-chip companies get their IT databases hacked or security breached - and they have the facility to spend millions on IT security.
"So considering these times of austerity we live in, I'm pretty sure that the council IT systems are not at a level of security that they should be even considering retaining children's identity, especially for something as simple as paying for their school dinner."
Those who choose not to participate in the programme can opt for a pin number choice instead, but the randomly generated four-digit number is not as secure as a fingerprint.
Angus, East Ayrshire, Edinburgh and West Lothian have already opted for fingerprint payments due to its ease and speed at the tills.
The system is becoming more popular across Scotland, despite fierce criticism from campaigners such as Big Brother Watch, who described the rise of its popularity as "alarming".
In 2006, Todholm Primary, Paisley, Renfrewshire, became the first in the world to introduce a similar palm-scanning system.
The cashless system was introduced by East Dunbartonshire Council in 1998 but has had a number of upgrades to keep up with technology updates, including the inclusion of the fingerprint scheme.
Depute chief executive of education, people & business for the council, Ann Davie, said: "The security of pupils' data is of paramount importance and the council continuously reviews its data protection policies and procedures in line with current legislation."