Advice published this week by Becta, the government's education technology agency, said that although they were not legally obliged to, schools should consult children and parents before introducing biometric systems.
It has been estimated that more than 3,500 schools make use of the fingerprints of their pupils in school canteens, libraries and for recording attendance.
"It is good practice for schools to be clear and open with all parents when introducing the technology," Becta advised.
"Schools should also reassure parents and pupils that they will not pass the data to any third parties and explain how the personal data used will be kept safe."
Headteachers were also advised to make it clear that all biometric data would be destroyed when children left.
Nick Gibb, shadow schools minister, described the guidance as very disappointing. "It is very weak as it neither requires schools to seek parental consent nor recognises the serious issues at stake with schools fingerprinting children simply for administrative convenience," he said. "The government needs to look more carefully at the fundamental principles these issues raise."
Jim Knight, the schools minister, said he had seen for himself how well biometric systems worked.
"They are able to speed up lunch queues, remove the need for children to carry money and take away the stigma of free school meals," said Mr Knight.
"Moreover, they can enable schools to register pupils more easily as they move from class to class."
A spokesman for Becta said that schools should be prepared to offer alternatives where parents strongly objected to a biometric system.
"In lunch queues this could be cash or a swipe card," he said.
Research by the Conservative party found last month that less than a quarter of local education authorities outlawed the use of biometric data.