The council stopped schools taking into account whether they were a family's first preference when choosing pupils this year. All authorities will have to take similiar action for admissions from September 2008.
Parents in Reigate have complained that the equal preference system has meant that about 20 children have missed out on places at the schools nearest to where they live. The council has offered them means-assessed taxi journeys to a school four miles away.
Jane Stevenson, mother of a four-year-old boy, Asa, was deeply worried.
"I'm not putting him into a taxi at his age," she said. "I looked into getting him a place at private school, but I can't afford it. I'm considering home schooling." The change has also upset parents of children starting secondary schools, who will have to travel even further.
About 20 children in villages south of Farnham have been offered secondary places up to 18 miles away, instead of at their local secondary school, Weydon.
And 31 children at Raleigh primary school in West Horsley have been offered places in three other towns - Guildford, Woking and Leatherhead - rather than at their local secondary.
Sarah Judd, whose 11-year-old daughter Ellie is affected, said: "We are devastated by this decision. It will split a very close community."
Andrew Crisp, Surrey council's executive member for education, said that the operation of the equal preference system would be reviewed this week.
"Although the old system was not perfect, it worked well," he said.