David Clouter set up the Leave Them Kids Alone campaign after getting a letter from St Matthew's primary in Cambridge that said the school intended to scan the thumbprint of his 11-year-old daughter Marysia.
Mr Clouter, a music consultant, was horrified that the school had planned to proceed without parents' permission. "It is an intrusion of personal privacy," he said.
"I also do not think that a school is a secure enough place to store such information - if someone got hold of it they could use it for identity theft at any point in my daughter's future. A fingerprint is not like a Pin number which you can simply change."
He said that his campaign has received backing from parents and pupils at other schools, from a professor of communications at Cambridge university and from David Howarth, the local MP.
But teachers have defended the systems, saying they make it easier for children to borrow library books and for staff to record attendance. They also say there have been few complaints from parents.
Two of the most popular systems are Junior Librarian, which has been available for four years and is used in around 3,500 UK schools to let pupils borrow books, and the more recent VeriCool (see report above), which 22 schools use for registration and cashless catering.
Both systems record a series of points on a fingerprint which are encrypted and deleted if a student leaves school. Even if a hacker were to crack the code, which the makers insist is impossible, they would not be able to recreate the fingerprint from the points.
Tony Davies, head of St Matthew's primary, has written to parents since Mr Clouter's initial complaints allowing them to opt out of using Junior Librarian.
Mr Davies said: "We have only had about a dozen parents say they do not want their children to use it, and a few of those changed their minds when they learned more about it."
Ash Grange primary in Surrey has been using Junior Librarian for four years without any complaints from parents. Jackie Chitson, librarian, said the programme had increased use of the library and reduced the number of books which pupils lost.
"The children love using it because it is very futuristic and it means they can take out books on their own," she said.
"Sometimes a child will say 'I didn't take that book home', but when they put their finger on the scanner the book cover appears on the screen and they remember that they did. Classrooms are getting interactive whiteboards, so why can't libraries be up-to-date as well?"
Paul Coase, business manager of VeriCool, said that the systems were safe and that children enjoyed using them because "they feel like they are in Doctor Who".
Sixth-formers at Edgbarrow school in Berkshire have claimed they are being threatened with expulsion if they refuse to use a thumbprint attendance system from September. But the claim has been rejected by the school, which insists the system will be optional.