The scheme is being trialled on junior classes at Higher Lane Primary in Whitefield, Bury, Greater Manchester.
Officials confirmed it is due to be extended to all pupils at the school, one of the areas largest primary schools, with 453 pupils aged four to 11.
School authorities defended the scheme on Thursday, and moved to reassure parents that the voluntary system, is heavily encrypted or coded and that no images of fingerprints would be stored.
But critics said they were “appalled” at the system, developed by Microsoft which is also being trialled in other parts of the country.
“This is quite clearly appalling,” said Phil Booth, national coordinator of NO2ID, a privacy campaign group.
“For such a trivial issue as taking out of library books the taking of fingerprints is way over the top and wrong.
“It conditions children to hand over sensitive personal information.”
He added: “The money for such a system could be spent on actual school resources. How about some more books for the library instead?
“This needs to be rolled back or stopped. I would argue there is no justification for such a scheme.
But Lesley Isherwood, the school headmaster, defended the system, saying it was introduced as a more efficient way of books being borrowed from the recently renovated library.
She confirmed it would be extended to all pupils, adding that parents would be given the choice to opt in or out.
"We have researched this scheme thoroughly. It is a biometric recognition system and no image of a fingerprint is ever stored. It is a voluntary system,” she said.
"The thumbprint creates a mathematical template. All parents have been written to and we have told them what the system is all about. From the responses we have had there has been overwhelming support."
She added: "We hold a lot of information about children because we are a school. This is no different."
All pupils' details are erased when they leave school.
It comes after schemes to fingerprint children as part of payment for their school dinners was introduced around the country.