From September, universal baseline assessment will be used to help teachers gauge reception pupils' ability in their first seven weeks.
Figures from Government advisers, however, reveal that girls consistently outstripped boys across the board in pilots, raising fears that four and five-year-old boys will be unfairly judged too quickly.
"The odds are stacked against boys from the start. There is a real danger teachers will identify whole cohorts as failures, writing them off before they've had a chance," said Madeline Portwood, senior educational psychologist at Durham Council.
Of the 6,732 children assessed, twice as many boys as girls fell into the bottom attainment category, failing to reach accepted standards. Girls outnumbered boys by about 30 per cent in the top group.
In number work, 35 per cent of girls reached the higher levels, compared with 29 per cent of boys. In reading and letter knowledge, a quarter reached the higher scores, compared with 16 per cent of boys.
Ms Portwood said: "It's no surprise girls score higher. It has nothing to do with intelligence. Boys simply develop at different levels. By key stage 2 it tends to have balanced out, but that might be too late for boys who have already been branded failures - disaffection sets in early."
Ms Portwood co-developed A Flying Start, Durham's baseline system, which has been adopted by six other local authorities.
David Hawker, head of curriculum and assessment at the Qualifications and Curriculum Authority with responsibility for under-fives work, said the differing scores could not be fully justified by developmental differences.
He said: "It is a phenomenon that boys develop differently to girls. We don't know why. But teachers shouldn't put differences down to slower development. That would be as crass as making excuses for poverty.
"The things we ask children to be able to do when they start school, such as knowing their alphabet, counting numbers up to 10, being socially adjusted -should be exactly the same for boys as for girls," Mr Hawker added.
Helen Penn, at the Thomas Coram Research Unit at the Institute of Education, said: "The real question isn't about gender. It's about why on earth we choose to grade children so early at all."