The listed Merseyside schools were unavailable for comment last night as they had closed for the summer holidays.
Though the two Liverpool schools are run by the Catholic Church and the Church of England, a spokesman for Liverpool City Council said fingerprinting was "not something the authority would encourage".
Executive member for education Cllr Paul Clein said the system was "frightening".
He continued: "If the system was proposed for Liverpool council schools, I would not support it.
"It's unnecessary. "Fingerprinting children will give them the impression they are under suspicion, as they so often are these days. They are increasingly treated as potential criminals.
"This country already has the biggest DNA database. There is already enough information about people without this."