The leavethemchildren alone.com website lists 200 schools where the system is in use, including St Anne's Church of England Primary School in Old Swan and Archbishop Beck Roman Catholic Secondary School in Walton.
It says fingerprints are also being taken at Bowring Comprehensive School in Huyton, Sutton High Sports College in St Helens and Great Sankey County High School in Warrington.
Dr John Whittaker, the UK Independence Party MEP for the North West, said he fears children's prints are being taken without their parents' knowledge.
He added: "Almost 30 schools in the North West are known to have fingerprinted their pupils.
"I want to know why it is being done, how widespread it is and whether it is being carried out at the behest of the local education authority.
"Most important of all, I want to know if schools are seeking the consent of parents before carrying out such actions.
"We really have reached a pitiful level in this country when we are fingerprinting children at primary schools and keeping their parents in the dark".